DB code: S00239

RLCP classification	6.10.398000.111 : Double-bonded atom exchange
	6.10.431300.120 : Double-bonded atom exchange
	8.121.1440000.6450 : Isomerization
	4.202.112900.6000 : Addition
	5.200.552010.6500 : Elimination
	5.1202.1504200.6501 : Elimination
	8.11121.166400.120 : Isomerization
CATH domain	3.20.20.70 : TIM Barrel	Catalytic domain
E.C.	4.2.1.24
CSA
M-CSA
MACiE

CATH domain	Related DB codes (homologues)
3.20.20.70 : TIM Barrel	S00215 S00217 S00218 S00219 S00532 S00198 S00220 S00745 S00537 S00538 S00539 S00826 S00841 S00235 S00240 S00243 S00244 S00199 S00200 S00201 S00221 S00222 S00847 S00224 S00225 S00226 D00014 D00029 M00141 T00015 T00239 D00664 D00665 D00804 D00863 T00089

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P0ACB2	Delta-aminolevulinic acid dehydratase	ALADH ALAD EC 4.2.1.24 Porphobilinogen synthase	NP_414903.4 (Protein) NC_000913.2 (DNA/RNA sequence) YP_488662.1 (Protein) NC_007779.1 (DNA/RNA sequence)	PF00490 (ALAD) [Graphical View]

KEGG enzyme name
porphobilinogen synthase aminolevulinate dehydratase delta-aminolevulinate dehydratase delta-aminolevulinic acid dehydrase delta-aminolevulinic acid dehydratase aminolevulinic dehydratase delta-aminolevulinic dehydratase 5-levulinic acid dehydratase 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate andcyclizing)

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P0ACB2	HEM2_ECOLI	2 5-aminolevulinate = porphobilinogen + 2 H(2)O.	Homooctamer.		Binds 1 magnesium ion per monomer. Binds 1 zinc ion per monomer.

KEGG Pathways
Map code	Pathways	E.C.
MAP00860	Porphyrin and chlorophyll metabolism

Compound table
	Cofactors		Substrates	Products		Intermediates
KEGG-id	C00038	C00305	C00430	C00931	C00001
E.C.
Compound	Zinc	Magnesium	5-Aminolevulinate	Porphobilinogen	H2O	P-side ALA carbinolamine transition-state	P-side ALA Schiff-base intermediate	A-side ALA carbinolamine + P-side ALA Schiff-base intermediate	A-side/P-side ALA Schiff-base intermediate	A-side enamine + P-side Schiff-base intermediate	C-C bonded intermediate	C-N bonded intermediate
Type	heavy metal	divalent metal (Ca2+, Mg2+)	amino acids,carbohydrate	amine group,aromatic ring (with nitrogen atoms),carboxyl group	H2O
ChEBI	29105 29105	18420 18420	17549 356416 17549 356416	17381 17381	15377 15377
PubChem	32051 32051	888 888	137 7048523 137 7048523	1021 1021	22247451 962 22247451 962

1b4eA	Bound:_ZN_400	Analogue:_ZN_401	Unbound	Unbound		Unbound	Intermediate-analogue:LEA	Unbound	Unbound	Unbound	Unbound	Unbound
1i8jA	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Unbound	Unbound	Intermediate-analogue:DSB	Unbound	Unbound	Unbound
1i8jB	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Unbound	Unbound	Intermediate-analogue:DSB	Unbound	Unbound	Unbound
1l6sA	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Unbound	Unbound	Intermediate-analogue:DSB	Unbound	Unbound	Unbound
1l6sB	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Unbound	Unbound	Intermediate-analogue:DSB	Unbound	Unbound	Unbound
1l6yA	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Intermediate-analogue:4OX	Unbound	Unbound	Unbound	Unbound	Unbound
1l6yB	Bound:_ZN	Bound:_MG	Unbound	Unbound		Unbound	Intermediate-analogue:4OX	Unbound	Unbound	Unbound	Unbound	Unbound

Reference for Active-site residues
resource	references	E.C.

Active-site residues
PDB	Catalytic residues	Cofactor-binding residues	Modified residues	Main-chain involved in catalysis	Comment

1b4eA	ASP 118;SER 165;LYS 195;LYS 247	CYS 120;CYS 122;CYS 130(Zinc binding);GLU 232(Magnesium binding)
1i8jA	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)
1i8jB	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)
1l6sA	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)
1l6sB	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)
1l6yA	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)
1l6yB	ASP 117;SER 164;LYS 194;LYS 246	CYS 119;CYS 121;CYS 129(Zinc binding);GLU 231(Magnesium binding)

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[1]	Scheme 2, p.285	5
[5]	Fig.1, p.8346
[7]	Fig.7, p.2122
[11]	Fig.1, Fig.2, p.11561
[13]	Fig.3, p.169-175	2
[17]	p.1027
[20]	Fig.7, p.4273-4275
[23]	Fig.1, p.599
[24]	Fig.6, p.1254
[25]	p.428
[27]	Fig.8, p.191-194	11
[28]	p.8234-8256
[29]	Fig.4, p.199-200	8
[31]	p.138-139
[33]	Scheme 2, p.589-590	7
[34]	p.19797-19798
[35]	Fig.6, p.243-245	10
[36]	Scheme 2, p.736-737	8
[38]	p.567-568
[41]	p.1225-1226
[42]	Fig.5, p.8251-8252

References
[1]
Resource
Comments
Medline ID
PubMed ID	6967019
Journal	FEBS Lett
Year	1980
Volume	114
Pages	283-6
Authors	Jordan PM, Seehra JS
Title	13C NMR as a probe for the study of enzyme-catalysed reactions: mechanism of action of 5-aminolevulinic acid dehydratase.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	3663587
Journal	Biochemistry
Year	1987
Volume	26
Pages	4258-64
Authors	Jaffe EK, Markham GD
Title	13C NMR studies of porphobilinogen synthase: observation of intermediates bound to a 280,000-dalton protein.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	3166990
Journal	Biochemistry
Year	1988
Volume	27
Pages	4475-81
Authors	Jaffe EK, Markham GD
Title	13C NMR studies of methylene and methine carbons of substrate bound to a 280,000-dalton protein, porphobilinogen synthase.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID	3242540
Journal	Biol Chem Hoppe Seyler
Year	1988
Volume	369
Pages	1099-103
Authors	Pilz I, Schwarz E, Vuga M, Beyersmann D
Title	Small angle X-ray scattering study on bovine porphobilinogen synthase (5-aminolaevulinate dehydratase).
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID	2252894
Journal	Biochemistry
Year	1990
Volume	29
Pages	8345-50
Authors	Jaffe EK, Markham GD, Rajagopalan JS
Title	15N and 13C NMR studies of ligands bound to the 280,000-dalton protein porphobilinogen synthase elucidate the structures of enzyme-bound product and a Schiff base intermediate.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	1965291
Journal	Biol Chem Hoppe Seyler
Year	1990
Volume	371
Pages	1145-52
Authors	Block C, Lohmann RD, Beyersmann D
Title	Probing of active site residues of the zinc enzyme 5-aminolevulinate dehydratase by spin and fluorescence labels.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID	1346974
Journal	Biochemistry
Year	1992
Volume	31
Pages	2113-23
Authors	Jaffe EK, Abrams WR, Kaempfen HX, Harris KA Jr
Title	5-Chlorolevulinate modification of porphobilinogen synthase identifies a potential role for the catalytic zinc.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	8424649
Journal	Arch Biochem Biophys
Year	1993
Volume	300
Pages	169-77
Authors	Mitchell LW, Jaffe EK
Title	Porphobilinogen synthase from Escherichia coli is a Zn(II) metalloenzyme stimulated by Mg(II).
Related PDB
Related UniProtKB
[9]
Resource
Comments	CHARACTERIZATION, AND SEQUENCE OF 1-5; 95-134 AND 237-253.
Medline ID	93176130
PubMed ID	8439296
Journal	Biochem J
Year	1993
Volume	290
Pages	279-87
Authors	Spencer P, Jordan PM
Title	Purification and characterization of 5-aminolaevulinic acid dehydratase from Escherichia coli and a study of the reactive thiols at the metal-binding domain.
Related PDB
Related UniProtKB	P15002
[10]
Resource
Comments
Medline ID
PubMed ID	8382991
Journal	Protein Sci
Year	1993
Volume	2
Pages	71-9
Authors	Markham GD, Myers CB, Harris KA Jr, Volin M, Jaffe EK
Title	Spatial proximity and sequence localization of the reactive sulfhydryls of porphobilinogen synthase.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID	7918369
Journal	Biochemistry
Year	1994
Volume	33
Pages	11554-62
Authors	Jaffe EK, Volin M, Myers CB, Abrams WR
Title	5-Chloro[1,4-13C]levulinic acid modification of mammalian and bacterial porphobilinogen synthase suggests an active site containing two Zn(II).
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID	7819203
Journal	Biochemistry
Year	1995
Volume	34
Pages	244-51
Authors	Jaffe EK, Ali S, Mitchell LW, Taylor KM, Volin M, Markham GD
Title	Characterization of the role of the stimulatory magnesium of Escherichia coli porphobilinogen synthase.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID	7592564
Journal	J Bioenerg Biomembr
Year	1995
Volume	27
Pages	169-79
Authors	Jaffe EK
Title	Porphobilinogen synthase, the first source of heme's asymmetry.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	7592604
Journal	J Biol Chem
Year	1995
Volume	270
Pages	24054-9
Authors	Mitchell LW, Volin M, Jaffe EK
Title	The phylogenetically conserved histidines of Escherichia coli porphobilinogen synthase are not required for catalysis.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	8612634
Journal	Eur J Biochem
Year	1996
Volume	236
Pages	600-8
Authors	Stolz M, Dornemann D
Title	Purification, metal cofactor, N-terminal sequence and subunit composition of a 5-aminolevulinic acid dehydratase from the unicellular green alga Scenedesmus obliquus, mutant C-2A'.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID	9341235
Journal	Biochemistry
Year	1997
Volume	36
Pages	13421-7
Authors	Petrovich RM, Jaffe EK
Title	Magnetic resonance studies on the active site and metal centers of Bradyrhizobium japonicum porphobilinogen synthase.
Related PDB
Related UniProtKB
[17]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID	98069651
PubMed ID	9406553
Journal	Nat Struct Biol
Year	1997
Volume	4
Pages	1025-31
Authors	Erskine PT, Senior N, Awan S, Lambert R, Lewis G, Tickle IJ, Sarwar M, Spencer P, Thomas P, Warren MJ, Shoolingin-Jordan PM, Wood SP, Cooper JB
Title	X-ray structure of 5-aminolaevulinate dehydratase, a hybrid aldolase.
Related PDB	1aw5
Related UniProtKB	P05373
[18]
Resource
Comments
Medline ID
PubMed ID	9260292
Journal	Protein Sci
Year	1997
Volume	6
Pages	1774-6
Authors	Erskine PT, Senior N, Maignan S, Cooper J, Lambert R, Lewis G, Spencer P, Awan S, Warren M, Tickle IJ, Thomas P, Wood SP, Shoolingin-Jordan PM
Title	Crystallization of 5-aminolaevulinic acid dehydratase from Escherichia coli and Saccharomyces cerevisiae and preliminary X-ray characterization of the crystals.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID	9766004
Journal	Biochem Soc Trans
Year	1998
Volume	26
Pages	S285
Authors	Norton E, Sarwar M, Shoolingin-Jordan P
Title	Mechanistic studies on E.coli 5-aminolaevulinic acid dehydratase.
Related PDB
Related UniProtKB
[20]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).
Medline ID	99211872
PubMed ID	10194344
Journal	Biochemistry
Year	1999
Volume	38
Pages	4266-76
Authors	Erskine PT, Norton E, Cooper JB, Lambert R, Coker A, Lewis G, Spencer P, Sarwar M, Wood SP, Warren MJ, Shoolingin-Jordan PM
Title	X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 A resolution.
Related PDB	1b4e
Related UniProtKB	P15002
[21]
Resource
Comments
Medline ID
PubMed ID	10529243
Journal	Biochemistry
Year	1999
Volume	38
Pages	13968-75
Authors	Frankenberg N, Heinz DW, Jahn D
Title	Production, purification, and characterization of a Mg2+-responsive porphobilinogen synthase from Pseudomonas aeruginosa.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID	10529244
Journal	Biochemistry
Year	1999
Volume	38
Pages	13976-82
Authors	Frankenberg N, Jahn D, Jaffe EK
Title	Pseudomonas aeruginosa contains a novel type V porphobilinogen synthase with no required catalytic metal ions.
Related PDB
Related UniProtKB
[23]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS).
Medline ID	99286289
PubMed ID	10356331
Journal	J Mol Biol
Year	1999
Volume	289
Pages	591-602
Authors	Frankenberg N, Erskine PT, Cooper JB, Shoolingin-Jordan PM, Jahn D, Heinz DW
Title	High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase.
Related PDB	1b4k
Related UniProtKB	Q59643
[24]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS).
Medline ID	99313446
PubMed ID	10386874
Journal	Protein Sci
Year	1999
Volume	8
Pages	1250-6
Authors	Erskine PT, Newbold R, Roper J, Coker A, Warren MJ, Shoolingin-Jordan PM, Wood SP, Cooper JB
Title	The Schiff base complex of yeast 5-aminolaevulinic acid dehydratase with laevulinic acid.
Related PDB	1ylv
Related UniProtKB	P05373
[25]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID	20207114
PubMed ID	10739915
Journal	Acta Crystallogr D Biol Crystallogr
Year	2000
Volume	56
Pages	421-30
Authors	Erskine PT, Duke EM, Tickle IJ, Senior NM, Warren MJ, Cooper JB
Title	MAD analyses of yeast 5-aminolaevulinate dehydratase: their use in structure determination and in defining the metal-binding sites.
Related PDB	1qmk 1qml 1qnv
Related UniProtKB	P05373
[26]
Resource
Comments
Medline ID
PubMed ID	10913315
Journal	Biochemistry
Year	2000
Volume	39
Pages	9018-29
Authors	Kervinen J, Dunbrack RL Jr, Litwin S, Martins J, Scarrow RC, Volin M, Yeung AT, Yoon E, Jaffe EK
Title	Porphobilinogen synthase from pea: expression from an artificial gene, kinetic characterization, and novel implications for subunit interactions.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID	10712932
Journal	Chem Biol
Year	2000
Volume	7
Pages	185-96
Authors	Jarret C, Stauffer F, Henz ME, Marty M, Luond RM, Bobalova J, Schurmann P, Neier R
Title	Inhibition of Escherichia coli porphobilinogen synthase using analogs of postulated intermediates.
Related PDB
Related UniProtKB
[28]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
Medline ID	21338255
PubMed ID	11444968
Journal	Biochemistry
Year	2001
Volume	40
Pages	8227-36
Authors	Kervinen J, Jaffe EK, Stauffer F, Neier R, Wlodawer A, Zdanov A
Title	Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity.
Related PDB	1i8j
Related UniProtKB	P15002
[29]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS).
Medline ID	21405508
PubMed ID	11513881
Journal	FEBS Lett
Year	2001
Volume	503
Pages	196-200
Authors	Erskine PT, Coates L, Newbold R, Brindley AA, Stauffer F, Wood SP, Warren MJ, Cooper JB, Shoolingin-Jordan PM, Neier R
Title	The X-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with two diacid inhibitors.
Related PDB	1eb3 1gjp
Related UniProtKB	P05373
[30]
Resource
Comments
Medline ID
PubMed ID	11032841
Journal	J Biol Chem
Year	2001
Volume	276
Pages	1538-44
Authors	Mitchell LW, Volin M, Martins J, Jaffe EK
Title	Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase.
Related PDB
Related UniProtKB
[31]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
Medline ID	21431818
PubMed ID	11545591
Journal	J Mol Biol
Year	2001
Volume	312
Pages	133-41
Authors	Erskine PT, Newbold R, Brindley AA, Wood SP, Shoolingin-Jordan PM, Warren MJ, Cooper JB
Title	The x-ray structure of yeast 5-aminolaevulinic acid dehydratase complexed with substrate and three inhibitors.
Related PDB	1h7n 1h7o 1h7p 1h7r
Related UniProtKB	P05373
[32]
Resource
Comments
Medline ID
PubMed ID	11275419
Journal	Toxicol Lett
Year	2001
Volume	119
Pages	27-37
Authors	Farina M, Folmer V, Bolzan RC, Andrade LH, Zeni G, Braga AL, Rocha JB
Title	Selenoxides inhibit delta-aminolevulinic acid dehydratase.
Related PDB
Related UniProtKB
[33]
Resource
Comments
Medline ID
PubMed ID	12196142
Journal	Biochem Soc Trans
Year	2002
Volume	30
Pages	584-90
Authors	Shoolingin-Jordan PM, Spencer P, Sarwar M, Erskine PE, Cheung KM, Cooper JB, Norton EB
Title	5-Aminolaevulinic acid dehydratase: metals, mutants and mechanism.
Related PDB
Related UniProtKB
[34]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS).
Medline ID	22028088
PubMed ID	11909869
Journal	J Biol Chem
Year	2002
Volume	277
Pages	19792-9
Authors	Jaffe EK, Kervinen J, Martins J, Stauffer F, Neier R, Wlodawer A, Zdanov A
Title	Species-specific inhibition of porphobilinogen synthase by 4-oxosebacic acid.
Related PDB	1l6s 1l6y
Related UniProtKB	P15002
[35]
Resource
Comments
Medline ID
PubMed ID	12079382
Journal	J Mol Biol
Year	2002
Volume	320
Pages	237-47
Authors	Frere F, Schubert WD, Stauffer F, Frankenberg N, Neier R, Jahn D, Heinz DW
Title	Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism.
Related PDB	1gzg
Related UniProtKB
[36]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (1.66 ANGSTROMS) OF MUTANT D139N.
Medline ID	22075365
PubMed ID	12777167
Journal	Biochem J
Year	2003
Volume	373
Pages	733-8
Authors	Erskine PT, Coates L, Butler D, Youell JH, Brindley AA, Wood SP, Warren MJ, Shoolingin-Jordan PM, Cooper JB
Title	X-ray structure of a putative reaction intermediate of 5-aminolaevulinic acid dehydratase.
Related PDB	1ohl
Related UniProtKB	Q59643
[37]
Resource
Comments
Medline ID
PubMed ID	12897770
Journal	Nat Struct Biol
Year	2003
Volume	10
Pages	757-63
Authors	Breinig S, Kervinen J, Stith L, Wasson AS, Fairman R, Wlodawer A, Zdanov A, Jaffe EK
Title	Control of tetrapyrrole biosynthesis by alternate quaternary forms of porphobilinogen synthase.
Related PDB	1pv8
Related UniProtKB
[38]
Resource
Comments
Medline ID
PubMed ID	15327955
Journal	J Mol Biol
Year	2004
Volume	342
Pages	563-70
Authors	Coates L, Beaven G, Erskine PT, Beale SI, Avissar YJ, Gill R, Mohammed F, Wood SP, Shoolingin-Jordan P, Cooper JB
Title	The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution.
Related PDB	1w1z
Related UniProtKB
[39]
Resource
Comments
Medline ID
PubMed ID	15644204
Journal	J Mol Biol
Year	2005
Volume	345
Pages	1059-70
Authors	Frere F, Reents H, Schubert WD, Heinz DW, Jahn D
Title	Tracking the evolution of porphobilinogen synthase metal dependence in vitro.
Related PDB	1w54 1w56 1w5m 1w5n 1w5o 1w5p 1w5q
Related UniProtKB
[40]
Resource
Comments
Medline ID
PubMed ID	16131755
Journal	Acta Crystallogr D Biol Crystallogr
Year	2005
Volume	61
Pages	1222-6
Authors	Erskine PT, Coates L, Newbold R, Brindley AA, Stauffer F, Beaven GD, Gill R, Coker A, Wood SP, Warren MJ, Shoolingin-Jordan PM, Neier R, Cooper JB
Title	Structure of yeast 5-aminolaevulinic acid dehydratase complexed with the inhibitor 5-hydroxylaevulinic acid.
Related PDB	2c1h
Related UniProtKB
[41]
Resource
Comments
Medline ID
PubMed ID	16304458
Journal	Acta Crystallogr D Biol Crystallogr
Year	2005
Volume	61
Pages	1594-8
Authors	Coates L, Beaven G, Erskine PT, Beale SI, Wood SP, Shoolingin-Jordan PM, Cooper JB
Title	Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor.
Related PDB	1w31
Related UniProtKB
[42]
Resource
Comments
Medline ID
PubMed ID	16819823
Journal	Biochemistry
Year	2006
Volume	45
Pages	8243-53
Authors	Frere F, Nentwich M, Gacond S, Heinz DW, Neier R, Frankenberg-Dinkel N
Title	Probing the active site of Pseudomonas aeruginosa porphobilinogen synthase using newly developed inhibitors.
Related PDB	2c13 2c14 2c15 2c16 2c18 2c19
Related UniProtKB

Comments
(A) Exchange of double-bonded atoms; Schiff-base formation between Lys246 and P-side ALA substrate (see [17], [27] and [31]): (A1) Lys194 acts as a modulator to lower the pKa of the nucleophile Lys246. There are several subfamilies of the homologous enzymes, such as zinc-dependent (S00239, S00538 in EzCatDB), and zinc-independent (S00537, S00539) subfamilies. This enzyme belongs to zinc-dependent subfamily. According to the literature [36], the reaction proceeds as follows: (A) Exchange of double-bonded atoms; Schiff-base formation between Lys246 and P-side ALA substrate: (B) Exchange of double-bonded atoms; Schiff-base formation between Lys194 and A-side ALA substrate: (C) Isomerization; Shift of double-bond from N=C-C to N-C=C, forming an enamine intermediate at A-side: (D) Addition (C-C bond formation): (E) Addition (C-N bond formation): (F) Eliminative double-bond formation (releasing Lys194 at A-side): (G) Eliminative double-bond formation (releasing Lys246 at P-side): (H) Isomerization; Shift of double-bonds from N=C-C=C-C to N-C=C-C=C: However, although the first two reactions (A-B) and the last reaction (H) seem to be common to all the homologous enzymes (S00537, S00538, S00539 in EzCatDB), the rest of the reactions (D-G) have not been elucidated yet. The detailed mechanism must be as follows: (A2) Lys246 makes a nucleophilic attack on the carbonyl carbon of the substrate, ALA, at P-side, leading to formation of a tetrahedral carbinolamine transition-state. The carbinolamine oxygen of the transition-state is stabilized by the positive charge of Lys194. (A3) Lys194 acts as a general acid to protonate the carbinolamine oxygen of the transition-state, leading to formation of hydroxyl group, and then acts as a general base to deprotonate the sidechain of Lys246. (A4) The lone pair of the amine nitrogen of Lys246 makes a nucleophilic attack on the carbon atom of the carbinolamine transition-state, forming a Schiff-base. At the same time, Lys194 acts as a general acid to protonate the hydroxyl group of the carbinolamine, to facilitate the elimination of water molecule. (B) Exchange of double-bonded atoms; Schiff-base formation between Lys194 and A-side ALA substrate: (B1) Unprotonated sidechain of Lys194 acts as a nucleophile to attack on the carbonyl carbon of the substrate, ALA, at A-side, leading to formation of a carbinolamine transition-state. The carbinolamine oxygen of the transition-state is stabilized by the positive charge of the amino group of the ALA substrate at A-side. (B2) The amino group of the ALA substrate at A-side might act as a general acid to protonate the carbinolamine oxygen of the transition-state, leading to formation of hydroxyl group, and then act as a general base to deprotonate the sidechain of Lys194. (B3) The lone pair of the amine nitrogen of Lys194 makes a nucleophilic attack on the carbon atom of the carbinolamine transition-state, forming a Schiff-base. At the same time, the amino group of the ALA acts as a general acid to protonate the hydroxyl group of the carbinolamine, to facilitate the elimination of water molecule. (C) Isomerization; Shift of double-bond from N=C-C to N-C=C, forming an enamine intermediate at A-side: (C1) Hydroxide bound to zinc ion acts as a strong base to deprotonate C3 methylene of the Schiff-base intermediate at A-side, leading to formation of an enamine intermediate. (E) Addition (C-N bond formation): (E1) The unprotonated amino group of the ALA at A-side acts as a general base to deprotonate the amino group of the ALA at P-side. (E2) The amino group of the ALA at P-side makes a nucleophilic attack on the Schiff base of A-side, forming a cyclic intermediate. (E3) The protonated amino group of the ALA at A-side acts as a general acid to protonate the sidechain amine group of Lys194 at A-side. (F) Eliminative double-bond formation (releasing Lys194 at A-side): (F1) Lys246, which is covalently bound to the cyclic intermediate, acts as a general base to deprotonate the C2 atom of the intermediate (or originally C3 atom of ALA at A-side), and then acts as a general acid to protonate the eliminated group, Lys210. (F2) At the same time, Lys210 is eliminated from the intermediate; E2-like reaction. (G) Eliminative double-bond formation (releasing Lys246 at P-side): (G1) Lys210 acts as a general acid to protonate the eliminated group, the amino group of Lys246. (G2) The lone pair of enamine of the intermediate push the electron to form a new double bond, facilitating the elimination of Lys246; E1-like reaction. (H) Isomerization; Shift of double-bonds from N=C-C=C-C to N-C=C-C=C: (H1) Electrophilic Schiff-base assisted reaction. Lys246 acts as a general base to the C4 methylene of the intermediate (or originally C5 atom of ALA at P-side), leading to the shift of double-bonds.

Comments

(A) Exchange of double-bonded atoms; Schiff-base formation between Lys246 and P-side ALA substrate (see [17], [27] and [31]):
(A1) Lys194 acts as a modulator to lower the pKa of the nucleophile Lys246.
There are several subfamilies of the homologous enzymes, such as zinc-dependent (S00239, S00538 in EzCatDB), and zinc-independent (S00537, S00539) subfamilies. This enzyme belongs to zinc-dependent subfamily.
According to the literature [36], the reaction proceeds as follows:
(A) Exchange of double-bonded atoms; Schiff-base formation between Lys246 and P-side ALA substrate:
(B) Exchange of double-bonded atoms; Schiff-base formation between Lys194 and A-side ALA substrate:
(C) Isomerization; Shift of double-bond from N=C-C to N-C=C, forming an enamine intermediate at A-side:
(D) Addition (C-C bond formation):
(E) Addition (C-N bond formation):
(F) Eliminative double-bond formation (releasing Lys194 at A-side):
(G) Eliminative double-bond formation (releasing Lys246 at P-side):
(H) Isomerization; Shift of double-bonds from N=C-C=C-C to N-C=C-C=C:
However, although the first two reactions (A-B) and the last reaction (H) seem to be common to all the homologous enzymes (S00537, S00538, S00539 in EzCatDB), the rest of the reactions (D-G) have not been elucidated yet.
The detailed mechanism must be as follows:
(A2) Lys246 makes a nucleophilic attack on the carbonyl carbon of the substrate, ALA, at P-side, leading to formation of a tetrahedral carbinolamine transition-state. The carbinolamine oxygen of the transition-state is stabilized by the positive charge of Lys194.
(A3) Lys194 acts as a general acid to protonate the carbinolamine oxygen of the transition-state, leading to formation of hydroxyl group, and then acts as a general base to deprotonate the sidechain of Lys246.
(A4) The lone pair of the amine nitrogen of Lys246 makes a nucleophilic attack on the carbon atom of the carbinolamine transition-state, forming a Schiff-base. At the same time, Lys194 acts as a general acid to protonate the hydroxyl group of the carbinolamine, to facilitate the elimination of water molecule.
(B) Exchange of double-bonded atoms; Schiff-base formation between Lys194 and A-side ALA substrate:
(B1) Unprotonated sidechain of Lys194 acts as a nucleophile to attack on the carbonyl carbon of the substrate, ALA, at A-side, leading to formation of a carbinolamine transition-state. The carbinolamine oxygen of the transition-state is stabilized by the positive charge of the amino group of the ALA substrate at A-side.
(B2) The amino group of the ALA substrate at A-side might act as a general acid to protonate the carbinolamine oxygen of the transition-state, leading to formation of hydroxyl group, and then act as a general base to deprotonate the sidechain of Lys194.
(B3) The lone pair of the amine nitrogen of Lys194 makes a nucleophilic attack on the carbon atom of the carbinolamine transition-state, forming a Schiff-base. At the same time, the amino group of the ALA acts as a general acid to protonate the hydroxyl group of the carbinolamine, to facilitate the elimination of water molecule.
(C) Isomerization; Shift of double-bond from N=C-C to N-C=C, forming an enamine intermediate at A-side:
(C1) Hydroxide bound to zinc ion acts as a strong base to deprotonate C3 methylene of the Schiff-base intermediate at A-side, leading to formation of an enamine intermediate.
(E) Addition (C-N bond formation):
(E1) The unprotonated amino group of the ALA at A-side acts as a general base to deprotonate the amino group of the ALA at P-side.
(E2) The amino group of the ALA at P-side makes a nucleophilic attack on the Schiff base of A-side, forming a cyclic intermediate.
(E3) The protonated amino group of the ALA at A-side acts as a general acid to protonate the sidechain amine group of Lys194 at A-side.
(F) Eliminative double-bond formation (releasing Lys194 at A-side):
(F1) Lys246, which is covalently bound to the cyclic intermediate, acts as a general base to deprotonate the C2 atom of the intermediate (or originally C3 atom of ALA at A-side), and then acts as a general acid to protonate the eliminated group, Lys210.
(F2) At the same time, Lys210 is eliminated from the intermediate; E2-like reaction.
(G) Eliminative double-bond formation (releasing Lys246 at P-side):
(G1) Lys210 acts as a general acid to protonate the eliminated group, the amino group of Lys246.
(G2) The lone pair of enamine of the intermediate push the electron to form a new double bond, facilitating the elimination of Lys246; E1-like reaction.
(H) Isomerization; Shift of double-bonds from N=C-C=C-C to N-C=C-C=C:
(H1) Electrophilic Schiff-base assisted reaction. Lys246 acts as a general base to the C4 methylene of the intermediate (or originally C5 atom of ALA at P-side), leading to the shift of double-bonds.

Created	Updated
2004-06-22	2010-05-19