DB code: S00254

RLCP classification	5.12.1132000.75 : Elimination
CATH domain	3.30.1360.20 : Gyrase A; domain 2	Catalytic domain
E.C.	4.2.1.96
CSA	1dco
M-CSA	1dco
MACiE	M0073

CATH domain	Related DB codes (homologues)

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	RefSeq	Pfam
P61459	Pterin-4-alpha-carbinolamine dehydratase	PHS EC 4.2.1.96 4-alpha-hydroxy-tetrahydropterin dehydratase Phenylalanine hydroxylase-stimulating protein Pterin carbinolamine dehydratase PCD Dimerization cofactor of hepatocyte nuclear factor 1-alpha Dimerization cofactor of HNF1 DCoH	NP_001007602.1 (Protein) NM_001007601.1 (DNA/RNA sequence)	PF01329 (Pterin_4a) [Graphical View]

KEGG enzyme name
4a-hydroxytetrahydrobiopterin dehydratase 4alpha-hydroxy-tetrahydropterin dehydratase pterin-4alpha-carbinolamine dehydratase 4a-hydroxytetrahydrobiopterin hydro-lyase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P61459	PHS_RAT	(6R)-6-(L-erythro-1,2-dihydroxypropyl)- 5,6,7,8-tetrahydro-4a-hydroxypterin = (6R)-6-(L-erythro-1,2- dihydroxypropyl)-7,8-dihydro-6H-pterin + H(2)O.	Homotetramer or homodimer.	Cytoplasm. Nucleus. Note=Cytoplasmic and/or nuclear.

KEGG Pathways
Map code	Pathways	E.C.

Compound table
	Substrates	Products		Intermediates
KEGG-id	C15522	C00268	C00001
E.C.
Compound	4a-Hydroxytetrahydrobiopterin	6,7-Dihydrobiopterin	H2O
Type	amine group,aromatic ring (with nitrogen atoms),carbohydrate	amide group,amine group,aromatic ring (with nitrogen atoms),carbohydrate	H2O
ChEBI			15377 15377
PubChem	46173804 46173804	133246 133246	22247451 962 22247451 962

1dchA	Unbound	Unbound
1dchB	Unbound	Unbound
1dchC	Unbound	Unbound
1dchD	Unbound	Unbound
1dchE	Unbound	Unbound
1dchF	Unbound	Unbound
1dchG	Unbound	Unbound
1dchH	Unbound	Unbound
1dcoA	Unbound	Unbound
1dcoB	Unbound	Unbound
1dcoC	Unbound	Unbound
1dcoD	Unbound	Unbound
1dcoE	Unbound	Unbound
1dcoF	Unbound	Unbound
1dcoG	Unbound	Unbound
1dcoH	Unbound	Unbound
1dcpA	Unbound	Bound:HBI
1dcpB	Unbound	Bound:HBI
1dcpC	Unbound	Bound:HBI
1dcpD	Unbound	Bound:HBI
1dcpE	Unbound	Bound:HBI
1dcpF	Unbound	Bound:HBI
1dcpG	Unbound	Bound:HBI
1dcpH	Unbound	Bound:HBI

Reference for Active-site residues
resource	references	E.C.
literature [7], [11] & [14]

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

1dchA	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchB	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchC	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchD	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchE	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchF	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchG	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dchH	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoA	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoB	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoC	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoD	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoE	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoF	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoG	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcoH	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpA	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpB	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpC	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpD	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpE	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpF	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpG	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81
1dcpH	GLU 58;HIS 62;HIS 63;HIS 80;ASP 89			HIS 80;GLU 81

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[7]	p.558
[9]	Scheme 2, p.861-863	2
[11]	Fig.6, p.1969-1970
[14]	Fig.7, p.11252-11254
[15]	Fig.4, p.1430	5

References
[1]
Resource
Comments	VARIANT HYPERPHENYLALANINEMIA ARG-81.
Medline ID	93356171
PubMed ID	8352282
Journal	Am J Hum Genet
Year	1993
Volume	53
Pages	768-74
Authors	Citron BA, Kaufman S, Milstien S, Naylor EW, Greene CL, Davis MD
Title	Mutation in the 4a-carbinolamine dehydratase gene leads to mild hyperphenylalaninemia with defective cofactor metabolism.
Related PDB
Related UniProtKB	P61459
[2]
Resource
Comments
Medline ID
PubMed ID	8504250
Journal	Curr Opin Genet Dev
Year	1993
Volume	3
Pages	246-53
Authors	Hansen LP, Crabtree GR
Title	Regulation of the HNF-1 homeodomain proteins by DCoH.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID	7727440
Journal	Biochemistry
Year	1995
Volume	34
Pages	5801-10
Authors	Rebrin I, Bailey SW, Boerth SR, Ardell MD, Ayling JE
Title	Catalytic characterization of 4a-hydroxytetrahydropterin dehydratase.
Related PDB
Related UniProtKB
[4]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
Medline ID	95262643
PubMed ID	7744010
Journal	EMBO J
Year	1995
Volume	14
Pages	2034-42
Authors	Ficner R, Sauer UH, Stier G, Suck D
Title	Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1.
Related PDB
Related UniProtKB	P61459
[5]
Resource
Comments
Medline ID
PubMed ID	7635153
Journal	Eur J Biochem
Year	1995
Volume	231
Pages	414-23
Authors	Koster S, Thony B, Macheroux P, Curtius HC, Heizmann CW, Pfleiderer W, Ghisla S
Title	Human pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor-1 alpha. Characterization and kinetic analysis of wild-type and mutant enzymes.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID	8001680
Journal	FEBS Lett
Year	1995
Volume	357
Pages	62-4
Authors	Ficner R, Sauer UH, Ceska TA, Stier G, Suck D
Title	Crystallization and preliminary crystallographic studies of recombinant dimerization cofactor of transcription factor HNF1/pterin-4 alpha-carbinolamine dehydratase from liver.
Related PDB
Related UniProtKB
[7]
Resource
Comments	X-ray crystallography
Medline ID
PubMed ID	7725101
Journal	Science
Year	1995
Volume	268
Pages	556-9
Authors	Endrizzi JA, Cronk JD, Wang W, Crabtree GR, Alber T
Title	Crystal structure of DCoH, a bifunctional, protein-binding transcriptional coactivator.
Related PDB	1dch
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID	8590013
Journal	Structure
Year	1995
Volume	3
Pages	531-4
Authors	Kim JL, Burley SK
Title	PCD/DCoH: more than a second molecular saddle.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID	8944775
Journal	Eur J Biochem
Year	1996
Volume	241
Pages	858-64
Authors	Koster S, Stier G, Ficner R, Holzer M, Curtius HC, Suck D, Ghisla S
Title	Location of the active site and proposed catalytic mechanism of pterin-4a-carbinolamine dehydratase.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID	8682201
Journal	FEBS Lett
Year	1996
Volume	389
Pages	35-9
Authors	Suck D, Ficner R
Title	Structure and function of PCD/DCoH, an enzyme with regulatory properties.
Related PDB
Related UniProtKB
[11]
Resource
Comments	X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID	97052967
PubMed ID	8897596
Journal	Protein Sci
Year	1996
Volume	5
Pages	1963-72
Authors	Cronk JD, Endrizzi JA, Alber T
Title	High-resolution structures of the bifunctional enzyme and transcriptional coactivator DCoH and its complex with a product analogue.
Related PDB	1dco 1dcp
Related UniProtKB	P61459
[12]
Resource
Comments
Medline ID
PubMed ID	8995521
Journal	J Mol Biol
Year	1997
Volume	265
Pages	20-9
Authors	Rhee KH, Stier G, Becker PB, Suck D, Sandaltzopoulos R
Title	The bifunctional protein DCoH modulates interactions of the homeodomain transcription factor HNF1 with nucleic acids.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID	9391049
Journal	Proc Natl Acad Sci U S A
Year	1997
Volume	94
Pages	13469-74
Authors	Johnen G, Kaufman S
Title	Studies on the enzymatic and transcriptional activity of the dimerization cofactor for hepatocyte nuclear factor 1.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	9698371
Journal	Biochemistry
Year	1998
Volume	37
Pages	11246-54
Authors	Rebrin I, Thony B, Bailey SW, Ayling JE
Title	Stereospecificity and catalytic function of histidine residues in 4a-hydroxy-tetrahydropterin dehydratase/DCoH.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	9894810
Journal	Biol Chem
Year	1998
Volume	379
Pages	1427-32
Authors	Koster S, Stier G, Kubasch N, Curtius HC, Ghisla S
Title	Pterin-4a-carbinolamine dehydratase from Pseudomonas aeruginosa: characterization, catalytic mechanism and comparison to the human enzyme.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID	10966642
Journal	Nat Struct Biol
Year	2000
Volume	7
Pages	744-8
Authors	Rose RB, Bayle JH, Endrizzi JA, Cronk JD, Crabtree GR, Alber T
Title	Structural basis of dimerization, coactivator recognition and MODY3 mutations in HNF-1alpha.
Related PDB
Related UniProtKB

Comments
According to the literature, the true substrate and products are 4a-hydroxy-tetrahydrobiopterin and dihydrobiopterin (C00268 in KEGG), plus water, although different compounds are annotated in the Swiss-prot and KEGG data. According to the literature [11] & [14], the catalytic reaction seems to proceed as follows: (1) The catalytic dyad, Glu58-His63, acts as a general base, which abstracts the N8 proton on the opposite side of the eliminated group, 4a-hydroxyl group, leading to the formation of an oxyanion, with the negative charge on the O4 atom next to the eliminated group. The negative charge is stabilized by the mainchain amide groups of His80 and Glu81. (2) A general acid should protonate the eliminated, 4a-hydroxyl group, to facilitate the elimination reaction. For 4a(R)-hydroxyl group, the catalytic dyad, Asp89-His62, acts as the general acid, whilst His80 functions for the 4a(S)-enantiomer (see [14]). (The 4a-carbon is tetrahedral in the substrate.) (3) The remaining proton at N5 must be abstracted by a solvent water, considering the active-site structure (see [14]). This protonation leads to the protonation to the N8 atom by His63, releasing the final product.

Comments

According to the literature, the true substrate and products are 4a-hydroxy-tetrahydrobiopterin and dihydrobiopterin (C00268 in KEGG), plus water, although different compounds are annotated in the Swiss-prot and KEGG data.
According to the literature [11] & [14], the catalytic reaction seems to proceed as follows:
(1) The catalytic dyad, Glu58-His63, acts as a general base, which abstracts the N8 proton on the opposite side of the eliminated group, 4a-hydroxyl group, leading to the formation of an oxyanion, with the negative charge on the O4 atom next to the eliminated group. The negative charge is stabilized by the mainchain amide groups of His80 and Glu81.
(2) A general acid should protonate the eliminated, 4a-hydroxyl group, to facilitate the elimination reaction. For 4a(R)-hydroxyl group, the catalytic dyad, Asp89-His62, acts as the general acid, whilst His80 functions for the 4a(S)-enantiomer (see [14]). (The 4a-carbon is tetrahedral in the substrate.)
(3) The remaining proton at N5 must be abstracted by a solvent water, considering the active-site structure (see [14]). This protonation leads to the protonation to the N8 atom by His63, releasing the final product.

Created	Updated
2004-04-04	2009-02-26