DB code: S00432

RLCP classification 1.13.7500.450 : Hydrolysis
CATH domain 3.60.15.10 : Metallo-beta-lactamase; Chain A Catalytic domain
E.C. 3.5.2.6
CSA
M-CSA
MACiE M0016

CATH domain Related DB codes (homologues)
3.60.15.10 : Metallo-beta-lactamase; Chain A S00515 S00431

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P04190 Beta-lactamase 2
EC 3.5.2.6
Beta-lactamase II
Penicillinase
Cephalosporinase
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
P04190 BLA2_BACCE A beta-lactam + H(2)O = a substituted beta- amino acid. Monomer. Binds 2 zinc ions per subunit. The enzyme can also function with only 1 zinc ion.

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
15377
PubChem 32051
22247451
962
1bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound
1bc2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound
1bmcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
1bmeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound
1bvtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_ZN Unbound Unbound Unbound Unbound
1dxkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
2bc2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN Unbound Unbound Unbound Unbound
3bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:_ZN 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
1bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASN 180 ASP 56;HIS 86;HIS 88;ASP 90;HIS 149;CYS 168;HIS 210(two Zinc binding)
1bc2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASN 180 ASP 56;HIS 86;HIS 88;ASP 90;HIS 149;CYS 168;HIS 210(two Zinc binding)
1bmcA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 90;ASN 180 ASP 56;HIS 86;HIS 88; ;HIS 149;;HIS 210(Zinc binding)
1bmeA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASN 180 ASP 56;HIS 86;HIS 88;ASP 90;HIS 149;CYS 168;HIS 210(two Zinc binding)
1bvtA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ;ASN 180 ASP 56;HIS 86;HIS 88;ASP 90;HIS 149;CYS 168;HIS 210(two Zinc binding)
1dxkA Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 90;ASN 180 ASP 56;HIS 86;HIS 88; ;HIS 149;;HIS 210(Zinc binding) mutant C168S
2bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 90;ASN 180 ASP 56;HIS 86;HIS 88; ;HIS 149;;HIS 210(Zinc binding) mutant C168CSD
2bc2B Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 90;ASN 180 ASP 56;HIS 86;HIS 88; ;HIS 149;;HIS 210(Zinc binding) mutant C168CSD
3bc2A Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 90;ASN 180 ASP 56;HIS 86;HIS 88; ;HIS 149;;HIS 210(Zinc binding) mutant C168CSD

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
Related UniProtKB
[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
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB
[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.
Related PDB
Related UniProtKB

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 this 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 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