DB code: S00515

RLCP classification	1.13.10000.1220 : Hydrolysis
CATH domain	3.60.15.10 : Metallo-beta-lactamase; Chain A	Catalytic domain
E.C.	3.5.2.6
CSA	1sml 2bmi
M-CSA	1sml 2bmi
MACiE	M0015 M0258

CATH domain	Related DB codes (homologues)
3.60.15.10 : Metallo-beta-lactamase; Chain A	S00431 S00432

Uniprot Enzyme Name
UniprotKB	Protein name	Synonyms	Pfam
P25910	Beta-lactamase type II	EC 3.5.2.6 Penicillinase Cephalosporinase Imipenem-cefoxitin hydrolyzing enzyme	PF00753 (Lactamase_B) [Graphical View]
P52699	Beta-lactamase IMP-1	EC 3.5.2.6 Beta-lactamase type II Penicillinase BLAIMP	PF00753 (Lactamase_B) [Graphical View]
P52700	Metallo-beta-lactamase L1	EC 3.5.2.6 Beta-lactamase type II Penicillinase	PF00753 (Lactamase_B) [Graphical View]

KEGG enzyme name
beta-lactamase penicillinase cephalosporinase neutrapen penicillin beta-lactamase exopenicillinase ampicillinase penicillin amido-beta-lactamhydrolase penicillinase I, II beta-lactamase I-III beta-lactamase A, B, C beta-lactamase AME I cephalosporin-beta-lactamase

UniprotKB: Accession Number	Entry name	Activity	Subunit	Subcellular location	Cofactor
P25910	BLAB_BACFR	A beta-lactam + H(2)O = a substituted beta- amino acid.	Monomer.		Binds 2 zinc ions per subunit.
P52699	BLAB_SERMA	A beta-lactam + H(2)O = a substituted beta- amino acid.			Binds 2 zinc ions per subunit (By similarity).
P52700	BLA1_STEMA	A beta-lactam + H(2)O = a substituted beta- amino acid.	Homotetramer.	Periplasm (Potential).	Binds 2 zinc ions per subunit.

KEGG Pathways
Map code	Pathways	E.C.
MAP00311	Penicillin and cephalosporin biosynthesis
MAP00312	beta-Lactam resistance

Compound table
	Cofactors	Substrates				Products	Intermediates
KEGG-id	C00038	C01866	C00395	C00875	C00001	C03806
E.C.
Compound	Zinc	beta-Lactam	Penicillin	Cephalosporin	H2O	Substituted beta-amino acid
Type	heavy metal	amide group	carboxyl group,peptide/protein,sulfide group	amide group,amine group,carboxyl group,sulfide group	H2O	amino acids
ChEBI	29105 29105				15377 15377
PubChem	32051 32051				22247451 962 22247451 962

1a7tA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1a7tB	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1a8tA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1a8tB	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1bmiA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1bmiB	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1znbA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1znbB	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
2bmiA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
2bmiB	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
2znbA	Analogue:2x_CD	Unbound	Unbound	Unbound		Unbound
2znbB	Analogue:2x_CD	Unbound	Unbound	Unbound		Unbound
3znbA	Bound:_ZN,Analogue;_HG	Unbound	Unbound	Unbound		Unbound
3znbB	Bound:_ZN,Analogue;_HG	Unbound	Unbound	Unbound		Unbound
4znbA	Bound:_ZN	Unbound	Unbound	Unbound		Unbound
4znbB	Bound:_ZN	Unbound	Unbound	Unbound		Unbound
1dd6A	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1dd6B	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound
1smlA	Bound:2x_ZN	Unbound	Unbound	Unbound		Unbound

Reference for Active-site residues
resource	references	E.C.
Swiss-prot & literature [14] & [15]

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

1a7tA	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1a7tB	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1a8tA	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1a8tB	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1bmiA	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1bmiB	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
1znbA	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
1znbB	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
2bmiA	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
2bmiB	ASN 176	ASP 52;HIS 82;HIS 84;ASP 86;HIS 145;CYS 164;HIS 206(Two zinc binding)
2znbA	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
2znbB	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
3znbA	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
3znbB	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)
4znbA	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;;HIS 223(Two zinc binding)			mutant C168S
4znbB	ASN 193	ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;;HIS 223(Two zinc binding)			mutant C168S
1dd6A	ASN 167	ASP 48;HIS 77;HIS 79;ASP 81;HIS 139;CYS 158;HIS 197(Two zinc binding)
1dd6B	ASN 167	ASP 48;HIS 77;HIS 79;ASP 81;HIS 139;CYS 158;HIS 197(Two zinc binding)
1smlA	ASN 196	ASP 53;HIS 84;HIS 86;ASP 88;HIS 160;ASP 184;HIS 225(Two zinc binding)

References for Catalytic Mechanism
References	Sections	No. of steps in catalysis
[3]	p.4917-4920
[4]	p.831-832
[5]	Fig.1	2
[6]	Fig.2
[8]	p.12408-12410, Fig.7
[9]	p.55-57
[10]	p.322
[11]	Fig.7, p.130-133	2
[14]	Scheme 5, p.10020-10022	2
[15]	Fig.6, Fig.7, p.618-620
[17]	p.1403-1405
[21]	p.1599
[24]	Scheme 4	1
[28]	p.710-711
[30]	Fig.6, p.656

References
[1]
Resource
Comments	X-ray crystallography (3.5 Angstroms)
Medline ID	88133841
PubMed ID	3124808
Journal	Biochem J
Year	1987
Volume	248
Pages	181-8
Authors	Sutton B.J., Artymiuk P.J., Cordero-Borboa A.E., Little C., Phillips D.C., Waley S.G
Title	An X-ray-crystallographic study of beta-lactamase II from Bacillus cereus at 0.35-nm resolution.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID	2501295
Journal	J Biol Chem
Year	1989
Volume	264
Pages	11682-7
Authors	Lim HM, Pene JJ
Title	Mutations affecting the catalytic activity of Bacillus cereus 5/B/6 beta-lactamase II.
Related PDB
Related UniProtKB
[3]
Resource
Comments	X-ray crystallography (2.5 Angstroms)
Medline ID	96067120
PubMed ID	7588620
Journal	EMBO J
Year	1995
Volume	14
Pages	4914-21
Authors	Carfi A, Pares S, Duee E, Galleni M, Duez C, Frere JM, Dideberg O
Title	The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.
Related PDB	1bmc
Related UniProtKB
[4]
Resource
Comments	X-ray crystallography (1.85 Angstroms)
Medline ID	96434328
PubMed ID	8805566
Journal	Structure
Year	1996
Volume	4
Pages	823-36
Authors	Concha NO, Rasmussen BA, Bush K, Herzberg O
Title	Crystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis.
Related PDB	1znb
Related UniProtKB
[5]
Resource
Comments	X-ray crystallography (Cd(2+)-bound;2.1 Angstroms, Hg(2+)-soaked zinc-containing;2.7 Angstroms)
Medline ID	98078582
PubMed ID	9416622
Journal	Protein Sci
Year	1997
Volume	6
Pages	2671-6
Authors	Concha NO, Rasmussen BA, Bush K, Herzberg O
Title	Crystal structures of the cadmium- and mercury-substituted metallo-beta-lactamase from Bacteroides fragilis.
Related PDB	2znb 3znb
Related UniProtKB
[6]
Resource
Comments	X-ray crystallography (complex with potent inhibitors)
Medline ID
PubMed ID	9545432
Journal	Chem Biol
Year	1998
Volume	5
Pages	185-96
Authors	Toney JH, Fitzgerald PM, Grover-Sharma N, Olson SH, May WJ, Sundelof JG, Vanderwall DE, Cleary KA, Grant SK, Wu JK, Kozarich JW, Pompliano DL, Hammond GG
Title	Antibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-beta-lactamase.
Related PDB	1a8t
Related UniProtKB
[7]
Resource
Comments	X-ray crystallography (1.85 Angstroms)
Medline ID	98244858
PubMed ID	9578564
Journal	Biochemistry
Year	1998
Volume	37
Pages	6791-800
Authors	Fitzgerald PM, Wu JK, Toney JH
Title	Unanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Related PDB	1a7t
Related UniProtKB
[8]
Resource
Comments	X-ray crystallography (1.9 Angstroms)
Medline ID	98400945
PubMed ID	9730812
Journal	Biochemistry
Year	1998
Volume	37
Pages	12404-11
Authors	Fabiane SM, Sohi MK, Wan T, Payne DJ, Bateson JH, Mitchell T, Sutton BJ
Title	Crystal structure of the zinc-dependent beta-lactamase from Bacillus cereus at 1.9 A resolution: binuclear active site with features of a mononuclear enzyme.
Related PDB	1bc2
Related UniProtKB
[9]
Resource
Comments	X-ray crystallography (2.0 Angstroms, orthorhombic crystal form)
Medline ID
PubMed ID	9761816
Journal	Acta Crystallogr D Biol Crystallogr
Year	1998
Volume	54
Pages	45-57
Authors	Carfi A, Duee E, Paul-Soto R, Galleni M, Frere JM, Dideberg O
Title	X-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.
Related PDB	1bmi 2bmi
Related UniProtKB
[10]
Resource
Comments	X-ray crystallography (1.85 Angstroms)
Medline ID	98437525
PubMed ID	9761898
Journal	Acta Crystallogr D Biol Crystallogr
Year	1998
Volume	54
Pages	313-23
Authors	Carfi A, Duee E, Galleni M, Frere JM, Dideberg O
Title	1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
Related PDB	1bme 1bvt
Related UniProtKB
[11]
Resource
Comments	X-ray crystallography (1.7 Angstroms)
Medline ID	99030465
PubMed ID	9811546
Journal	J Mol Biol
Year	1998
Volume	284
Pages	125-36
Authors	Ullah JH, Walsh TR, Taylor IA, Emery DC, Verma CS, Gamblin SJ, Spencer J
Title	The crystal structure of the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia at 1.7 A resolution.
Related PDB	1sml
Related UniProtKB
[12]
Resource
Comments	X-ray crystallography (2.6 Angstroms, active site mutation)
Medline ID	99224909
PubMed ID	10210203
Journal	Protein Sci
Year	1999
Volume	8
Pages	249-52
Authors	Li Z, Rasmussen BA, Herzberg O
Title	Structural consequences of the active site substitution Cys181 ==> Ser in metallo-beta-lactamase from Bacteroides fragilis.
Related PDB	4znb
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID	10336469
Journal	J Biol Chem
Year	1999
Volume	274
Pages	15706-11
Authors	Yang Y, Keeney D, Tang X, Canfield N, Rasmussen BA
Title	Kinetic properties and metal content of the metallo-beta-lactamase CcrA harboring selective amino acid substitutions.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID	10433708
Journal	Biochemistry
Year	1999
Volume	38
Pages	10013-23
Authors	Wang Z, Fast W, Benkovic SJ
Title	On the mechanism of the metallo-beta-lactamase from Bacteroides fragilis.
Related PDB
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID	10508665
Journal	Curr Opin Chem Biol
Year	1999
Volume	3
Pages	614-22
Authors	Wang Z, Fast W, Valentine AM, Benkovic SJ
Title	Metallo-beta-lactamase: structure and mechanism.
Related PDB
Related UniProtKB
[16]
Resource
Comments	X-ray crystallography (native;3.1 Angstroms, complex with inhibitor;2.0 Angstroms)
Medline ID
PubMed ID	10757977
Journal	Biochemistry
Year	2000
Volume	39
Pages	4288-98
Authors	Concha NO, Janson CA, Rowling P, Pearson S, Cheever CA, Clarke BP, Lewis C, Galleni M, Frere JM, Payne DJ, Bateson JH, Abdel-Meguid SS
Title	Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor.
Related PDB	1dd6
Related UniProtKB
[17]
Resource
Comments	X-ray crystallography (1.85 Angstroms, active site mutation)
Medline ID	20386639
PubMed ID	10933508
Journal	Protein Sci
Year	2000
Volume	9
Pages	1402-6
Authors	Chantalat L, Duee E, Galleni M, Frere JM, Dideberg O
Title	Structural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.
Related PDB	1dxk
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID	11327823
Journal	Biochemistry
Year	2001
Volume	40
Pages	1640-50
Authors	Fast W, Wang Z, Benkovic SJ
Title	Familial mutations and zinc stoichiometry determine the rate-limiting step of nitrocefin hydrolysis by metallo-beta-lactamase from Bacteroides fragilis.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID	11439042
Journal	J Am Chem Soc
Year	2001
Volume	123
Pages	6555-63
Authors	Kaminskaia NV, Spingler B, Lippard SJ
Title	Intermediate in beta-lactam hydrolysis catalyzed by a dinuclear zinc(II) complex: relevance to the mechanism of metallo-beta-lactamase.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID	11443136
Journal	J Biol Chem
Year	2001
Volume	276
Pages	33638-44
Authors	Spencer J, Clarke AR, Walsh TR
Title	Novel mechanism of hydrolysis of therapeutic beta-lactams by Stenotrophomonas maltophilia L1 metallo-beta-lactamase.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID	11457108
Journal	J Am Chem Soc
Year	2001
Volume	123
Pages	3759-70
Authors	Suarez D, Merz KM Jr
Title	Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID	11484222
Journal	Proteins
Year	2001
Volume	44
Pages	448-59
Authors	Salsbury FR Jr, Crowley MF, Brooks CL 3rd
Title	Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID	11551939
Journal	J Biol Chem
Year	2001
Volume	276
Pages	45065-78
Authors	de Seny D, Heinz U, Wommer S, Kiefer M, Meyer-Klaucke W, Galleni M, Frere JM, Bauer R, Adolph HW
Title	Metal ion binding and coordination geometry for wild type and mutants of metallo-beta -lactamase from Bacillus cereus 569/H/9 (BcII): a combined thermodynamic, kinetic, and spectroscopic approach.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID	11583551
Journal	J Am Chem Soc
Year	2001
Volume	123
Pages	9867-79
Authors	Diaz N, Suarez D, Merz KM Jr
Title	Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.
Related PDB
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[25]
Resource
Comments	Identification of critical residues
Medline ID
PubMed ID	11714924
Journal	Protein Sci
Year	2001
Volume	10
Pages	2556-65
Authors	Materon IC, Palzkill T
Title	Identification of residues critical for metallo-beta-lactamase function by codon randomization and selection.
Related PDB
Related UniProtKB
[26]
Resource
Comments	Metal site
Medline ID
PubMed ID	11847294
Journal	Protein Sci
Year	2002
Volume	11
Pages	707-12
Authors	Gomes CM, Frazao C, Xavier AV, Legall J, Teixeira M
Title	Functional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID	12022865
Journal	Biochemistry
Year	2002
Volume	41
Pages	6615-30
Authors	Suarez D, Brothers EN, Merz KM Jr
Title	Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID	12203007
Journal	J Biol Inorg Chem
Year	2002
Volume	7
Pages	704-12
Authors	Dal Peraro M, Vila AJ, Carloni P
Title	Structural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID	12395427
Journal	J Comput Chem
Year	2002
Volume	23
Pages	1587-600
Authors	Suarez D, Diaz N, Merz KM Jr
Title	Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem.
Related PDB
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[30]
Resource
Comments
Medline ID
PubMed ID	12507470
Journal	J Mol Biol
Year	2003
Volume	325
Pages	651-60
Authors	Garcia-Saez I, Mercuri PS, Papamicael C, Kahn R, Frere JM, Galleni M, Rossolini GM, Dideberg O
Title	Three-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril.
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[31]
Resource
Comments
Medline ID
PubMed ID	12543663
Journal	Antimicrob Agents Chemother
Year	2003
Volume	47
Pages	582-7
Authors	Murphy TA, Simm AM, Toleman MA, Jones RN, Walsh TR
Title	Biochemical characterization of the acquired metallo-beta-lactamase SPM-1 from Pseudomonas aeruginosa.
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[32]
Resource
Comments
Medline ID
PubMed ID	12578382
Journal	Biochemistry
Year	2003
Volume	42
Pages	1673-83
Authors	Siemann S, Clarke AJ, Viswanatha T, Dmitrienko GI
Title	Thiols as classical and slow-binding inhibitors of IMP-1 and other binuclear metallo-beta-lactamases.
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[33]
Resource
Comments
Medline ID
PubMed ID	12611529
Journal	Inorg Chem
Year	2003
Volume	42
Pages	1604-15
Authors	Boerzel H, Koeckert M, Bu W, Spingler B, Lippard SJ
Title	Zinc-bound thiolate-disulfide exchange: a strategy for inhibiting metallo-beta-lactamases.
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[34]
Resource
Comments
Medline ID
PubMed ID	12684522
Journal	J Biol Chem
Year	2003
Volume	278
Pages	23868-73
Authors	Garcia-Saez I, Hopkins J, Papamicael C, Franceschini N, Amicosante G, Rossolini GM, Galleni M, Frere JM, Dideberg O
Title	The 1.5-A structure of Chryseobacterium meningosepticum zinc beta-lactamase in complex with the inhibitor, D-captopril.
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[35]
Resource
Comments
Medline ID
PubMed ID	12724330
Journal	J Biol Chem
Year	2003
Volume	278
Pages	29240-51
Authors	Damblon C, Jensen M, Ababou A, Barsukov I, Papamicael C, Schofield CJ, Olsen L, Bauer R, Roberts GC
Title	The inhibitor thiomandelic acid binds to both metal ions in metallo-beta-lactamase and induces positive cooperativity in metal binding.
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[36]
Resource
Comments
Medline ID
PubMed ID	12826725
Journal	Protein Eng
Year	2003
Volume	16
Pages	341-50
Authors	Oelschlaeger P, Schmid RD, Pleiss J
Title	Insight into the mechanism of the IMP-1 metallo-beta-lactamase by molecular dynamics simulations.
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Comments
This enzyme belongs to the class-B beta-lactamase (metallo-beta-lactamase) family. According to the literature [9] & [15], there are three types of metallo-beta-lactamases. (1) Enzyme from B. cereus: active with one zinc ion, and the binding of the second zinc increases its activity. (2) Enzyme from B. fragilis: active with two zinc ion. (3) Enzyme from A. hydrophilia: active with one zinc ion, and inhibited by the second zinc ion. Thus, the catalytic mechanism of the monozinc form is different from that of the dizinc form. According to the literature [3] & [15], the catalytic mechanism of the monozinc enzyme (S00432) is proposed as follows: (a) Zinc pre-forms the nucleophilic hydroxide, in combination with Asp90. (b) Zinc-bound hydroxide acts as a nucleophile to attack the carbonyl carbon, leading to a dianionic tetrahedral intermediate. (c) Zinc stabilizes the oxyanion of the dianionic intermediate, along with Asn180. (d) Asp90 deprotonates the anionic intermediate, to yield a dianionic tetrahedral intermediate, as a general base. (e) The breakdown of the dianionic tetrahedral intermediate is facilitated by protonation from Asp90 as a general acid. On the other hand, according to the literature [14] & [15], the catalytic mechanism of this dizinc enzyme (S00515) is as follows: (a) Zn1-bound hydroxide acts as a nucleophile to attack the carbonyl carbon. (b) Cleavage of the C-N bond results in a negatively charged nitrogen leaving group. (c) Asn193 stabilizes the carbonyl oxygen, together with Zn1. (d) Zn2 stabilizes the negatively charged leaving group, acting as a superacid. (e) Protonation of the negatively charged nitrogen by a second water molecule from solvent leads to the breakdown of the intermediate. (This protonation prior to the C-N bond cleavage is not required.) The paper [9] suggested that there had been an evolutionary pathway from a monozinc enzyme (A. hydrophilia) through an enzyme with one or two zinc ions (B. cereus: S00432) to a dizinc enzyme (B. fragilis: S00515).

Comments

This enzyme belongs to the class-B beta-lactamase (metallo-beta-lactamase) family.
According to the literature [9] & [15], there are three types of metallo-beta-lactamases.
(1) Enzyme from B. cereus: active with one zinc ion, and the binding of the second zinc increases its activity.
(2) Enzyme from B. fragilis: active with two zinc ion.
(3) Enzyme from A. hydrophilia: active with one zinc ion, and inhibited by the second zinc ion.
Thus, the catalytic mechanism of the monozinc form is different from that of the dizinc form.
According to the literature [3] & [15], the catalytic mechanism of the monozinc enzyme (S00432) is proposed as follows:
(a) Zinc pre-forms the nucleophilic hydroxide, in combination with Asp90.
(b) Zinc-bound hydroxide acts as a nucleophile to attack the carbonyl carbon, leading to a dianionic tetrahedral intermediate.
(c) Zinc stabilizes the oxyanion of the dianionic intermediate, along with Asn180.
(d) Asp90 deprotonates the anionic intermediate, to yield a dianionic tetrahedral intermediate, as a general base.
(e) The breakdown of the dianionic tetrahedral intermediate is facilitated by protonation from Asp90 as a general acid.
On the other hand, according to the literature [14] & [15], the catalytic mechanism of this dizinc enzyme (S00515) is as follows:
(a) Zn1-bound hydroxide acts as a nucleophile to attack the carbonyl carbon.
(b) Cleavage of the C-N bond results in a negatively charged nitrogen leaving group.
(c) Asn193 stabilizes the carbonyl oxygen, together with Zn1.
(d) Zn2 stabilizes the negatively charged leaving group, acting as a superacid.
(e) Protonation of the negatively charged nitrogen by a second water molecule from solvent leads to the breakdown of the intermediate. (This protonation prior to the C-N bond cleavage is not required.)
The paper [9] suggested that there had been an evolutionary pathway from a monozinc enzyme (A. hydrophilia) through an enzyme with one or two zinc ions (B. cereus: S00432) to a dizinc enzyme (B. fragilis: S00515).

Created	Updated
2002-09-04	2009-02-26