EzCatDB: S00515

DB codeS00515
RLCP classification1.13.10000.1220
CATH domainDomain 13.60.15.10Catalytic domain
E.C.3.5.2.6
CSA1sml,2bmi
MACiEM0015,M0258

CATH domainRelated DB codes (homologues)
3.60.15.10S00431,S00432

Enzyme Name
Swiss-protKEGG

P25910P52699P52700
Protein nameBeta-lactamase type IIBeta-lactamase IMP-1Metallo-beta-lactamase L1beta-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
SynonymsEC 3.5.2.6
Penicillinase
Cephalosporinase
Imipenem-cefoxitin hydrolyzing enzyme
EC 3.5.2.6
Beta-lactamase type II
Penicillinase
BLAIMP
EC 3.5.2.6
Beta-lactamase type II
Penicillinase

KEGG pathways
MAP codePathways
MAP00311Penicillin and cephalosporin biosynthesis
MAP00312beta-Lactam resistance

Swiss-prot:Accession NumberP25910P52699P52700
Entry nameBLAB_BACFRBLAB_SERMABLA1_STEMA
ActivityA beta-lactam + H(2)O = a substituted beta- amino acid.A beta-lactam + H(2)O = a substituted beta- amino acid.A beta-lactam + H(2)O = a substituted beta- amino acid.
SubunitMonomer.
Homotetramer.
Subcellular location

Periplasm (Potential).
CofactorBinds 2 zinc ions per subunit.Binds 2 zinc ions per subunit (By similarity).Binds 2 zinc ions per subunit.


CofactorsSubstratesProducts
KEGG-idC00038C01866C00395C00875C00001C03806
CompoundZincbeta-LactamPenicillinCephalosporinH2OSubstituted beta-amino acid
Typeheavy metalamide groupcarboxyl group,peptide/protein,sulfide groupamide group,amine group,carboxyl group,sulfide groupH2Oamino acids
1a7tABound:2x_ZNUnboundUnboundUnbound
Unbound
1a7tBBound:2x_ZNUnboundUnboundUnbound
Unbound
1a8tABound:2x_ZNUnboundUnboundUnbound
Unbound
1a8tBBound:2x_ZNUnboundUnboundUnbound
Unbound
1bmiABound:2x_ZNUnboundUnboundUnbound
Unbound
1bmiBBound:2x_ZNUnboundUnboundUnbound
Unbound
1znbABound:2x_ZNUnboundUnboundUnbound
Unbound
1znbBBound:2x_ZNUnboundUnboundUnbound
Unbound
2bmiABound:2x_ZNUnboundUnboundUnbound
Unbound
2bmiBBound:2x_ZNUnboundUnboundUnbound
Unbound
2znbAAnalogue:2x_CDUnboundUnboundUnbound
Unbound
2znbBAnalogue:2x_CDUnboundUnboundUnbound
Unbound
3znbABound:_ZN,Analogue;_HGUnboundUnboundUnbound
Unbound
3znbBBound:_ZN,Analogue;_HGUnboundUnboundUnbound
Unbound
4znbABound:_ZNUnboundUnboundUnbound
Unbound
4znbBBound:_ZNUnboundUnboundUnbound
Unbound
1dd6ABound:2x_ZNUnboundUnboundUnbound
Unbound
1dd6BBound:2x_ZNUnboundUnboundUnbound
Unbound
1smlABound:2x_ZNUnboundUnboundUnbound
Unbound

Active-site residues
resource
Swiss-prot & literature [14] & [15]
pdbCatalytic residuesCofactor-binding residuescomment
1a7tAASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1a7tBASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1a8tAASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1a8tBASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1bmiAASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1bmiBASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

1znbAASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

1znbBASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

2bmiAASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

2bmiBASN 176
ASP 52;HIS 82;HIS  84;ASP  86;HIS 145;CYS 164;HIS 206(Two zinc binding)

2znbAASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

2znbBASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

3znbAASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

3znbBASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;CYS 181;HIS 223(Two zinc binding)

4znbAASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;       ;HIS 223(Two zinc binding)
mutant C168S
4znbBASN 193
ASP 69;HIS 99;HIS 101;ASP 103;HIS 162;       ;HIS 223(Two zinc binding)
mutant C168S
1dd6AASN 167
ASP 48;HIS 77;HIS  79;ASP  81;HIS 139;CYS 158;HIS 197(Two zinc binding)

1dd6BASN 167
ASP 48;HIS 77;HIS  79;ASP  81;HIS 139;CYS 158;HIS 197(Two zinc binding)

1smlAASN 196
ASP 53;HIS 84;HIS  86;ASP  88;HIS 160;ASP 184;HIS 225(Two zinc binding)


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[3]p.4917-4920
[4]p.831-832
[5]Fig.12
[6]Fig.2
[8]p.12408-12410, Fig.7
[9]p.55-57
[10]p.322
[11]Fig.7, p.130-1332
[14]Scheme 5, p.10020-100222
[15]Fig.6, Fig.7, p.618-620
[17]p.1403-1405
[21]p.1599
[24]Scheme 41
[28]p.710-711
[30]Fig.6, p.656

references
[1]
CommentsX-ray crystallography (3.5 Angstroms)
Medline ID88133841
PubMed ID3124808
JournalBiochem J
Year1987
Volume248
Pages181-8
AuthorsSutton B.J., Artymiuk P.J., Cordero-Borboa A.E., Little C., Phillips D.C., Waley S.G
TitleAn X-ray-crystallographic study of beta-lactamase II from Bacillus cereus at 0.35-nm resolution.
[2]
PubMed ID2501295
JournalJ Biol Chem
Year1989
Volume264
Pages11682-7
AuthorsLim HM, Pene JJ
TitleMutations affecting the catalytic activity of Bacillus cereus 5/B/6 beta-lactamase II.
[3]
CommentsX-ray crystallography (2.5 Angstroms)
Medline ID96067120
PubMed ID7588620
JournalEMBO J
Year1995
Volume14
Pages4914-21
AuthorsCarfi A, Pares S, Duee E, Galleni M, Duez C, Frere JM, Dideberg O
TitleThe 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold.
Related PDB1bmc
[4]
CommentsX-ray crystallography (1.85 Angstroms)
Medline ID96434328
PubMed ID8805566
JournalStructure
Year1996
Volume4
Pages823-36
AuthorsConcha NO, Rasmussen BA, Bush K, Herzberg O
TitleCrystal structure of the wide-spectrum binuclear zinc beta-lactamase from Bacteroides fragilis.
Related PDB1znb
[5]
CommentsX-ray crystallography (Cd(2+)-bound;2.1 Angstroms, Hg(2+)-soaked zinc-containing;2.7 Angstroms)
Medline ID98078582
PubMed ID9416622
JournalProtein Sci
Year1997
Volume6
Pages2671-6
AuthorsConcha NO, Rasmussen BA, Bush K, Herzberg O
TitleCrystal structures of the cadmium- and mercury-substituted metallo-beta-lactamase from Bacteroides fragilis.
Related PDB2znb,3znb
[6]
CommentsX-ray crystallography (complex with potent inhibitors)
PubMed ID9545432
JournalChem Biol
Year1998
Volume5
Pages185-96
AuthorsToney 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
TitleAntibiotic sensitization using biphenyl tetrazoles as potent inhibitors of Bacteroides fragilis metallo-beta-lactamase.
Related PDB1a8t
[7]
CommentsX-ray crystallography (1.85 Angstroms)
Medline ID98244858
PubMed ID9578564
JournalBiochemistry
Year1998
Volume37
Pages6791-800
AuthorsFitzgerald PM, Wu JK, Toney JH
TitleUnanticipated inhibition of the metallo-beta-lactamase from Bacteroides fragilis by 4-morpholineethanesulfonic acid (MES): a crystallographic study at 1.85-A resolution.
Related PDB1a7t
[8]
CommentsX-ray crystallography (1.9 Angstroms)
Medline ID98400945
PubMed ID9730812
JournalBiochemistry
Year1998
Volume37
Pages12404-11
AuthorsFabiane SM, Sohi MK, Wan T, Payne DJ, Bateson JH, Mitchell T, Sutton BJ
TitleCrystal 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 PDB1bc2
[9]
CommentsX-ray crystallography (2.0 Angstroms, orthorhombic crystal form)
PubMed ID9761816
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages45-57
AuthorsCarfi A, Duee E, Paul-Soto R, Galleni M, Frere JM, Dideberg O
TitleX-ray structure of the ZnII beta-lactamase from Bacteroides fragilis in an orthorhombic crystal form.
Related PDB1bmi,2bmi
[10]
CommentsX-ray crystallography (1.85 Angstroms)
Medline ID98437525
PubMed ID9761898
JournalActa Crystallogr D Biol Crystallogr
Year1998
Volume54
Pages313-23
AuthorsCarfi A, Duee E, Galleni M, Frere JM, Dideberg O
Title1.85 A resolution structure of the zinc (II) beta-lactamase from Bacillus cereus.
Related PDB1bme,1bvt
[11]
CommentsX-ray crystallography (1.7 Angstroms)
Medline ID99030465
PubMed ID9811546
JournalJ Mol Biol
Year1998
Volume284
Pages125-36
AuthorsUllah JH, Walsh TR, Taylor IA, Emery DC, Verma CS, Gamblin SJ, Spencer J
TitleThe crystal structure of the L1 metallo-beta-lactamase from Stenotrophomonas maltophilia at 1.7 A resolution.
Related PDB1sml
[12]
CommentsX-ray crystallography (2.6 Angstroms, active site mutation)
Medline ID99224909
PubMed ID10210203
JournalProtein Sci
Year1999
Volume8
Pages249-52
AuthorsLi Z, Rasmussen BA, Herzberg O
TitleStructural consequences of the active site substitution Cys181 ==> Ser in metallo-beta-lactamase from Bacteroides fragilis.
Related PDB4znb
[13]
PubMed ID10336469
JournalJ Biol Chem
Year1999
Volume274
Pages15706-11
AuthorsYang Y, Keeney D, Tang X, Canfield N, Rasmussen BA
TitleKinetic properties and metal content of the metallo-beta-lactamase CcrA harboring selective amino acid substitutions.
[14]
PubMed ID10433708
JournalBiochemistry
Year1999
Volume38
Pages10013-23
AuthorsWang Z, Fast W, Benkovic SJ
TitleOn the mechanism of the metallo-beta-lactamase from Bacteroides fragilis.
[15]
PubMed ID10508665
JournalCurr Opin Chem Biol
Year1999
Volume3
Pages614-22
AuthorsWang Z, Fast W, Valentine AM, Benkovic SJ
TitleMetallo-beta-lactamase: structure and mechanism.
[16]
CommentsX-ray crystallography (native;3.1 Angstroms, complex with inhibitor;2.0 Angstroms)
PubMed ID10757977
JournalBiochemistry
Year2000
Volume39
Pages4288-98
AuthorsConcha NO, Janson CA, Rowling P, Pearson S, Cheever CA, Clarke BP, Lewis C, Galleni M, Frere JM, Payne DJ, Bateson JH, Abdel-Meguid SS
TitleCrystal 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 PDB1dd6
[17]
CommentsX-ray crystallography (1.85 Angstroms, active site mutation)
Medline ID20386639
PubMed ID10933508
JournalProtein Sci
Year2000
Volume9
Pages1402-6
AuthorsChantalat L, Duee E, Galleni M, Frere JM, Dideberg O
TitleStructural effects of the active site mutation cysteine to serine in Bacillus cereus zinc-beta-lactamase.
Related PDB1dxk
[18]
PubMed ID11327823
JournalBiochemistry
Year2001
Volume40
Pages1640-50
AuthorsFast W, Wang Z, Benkovic SJ
TitleFamilial mutations and zinc stoichiometry determine the rate-limiting step of nitrocefin hydrolysis by metallo-beta-lactamase from Bacteroides fragilis.
[19]
PubMed ID11439042
JournalJ Am Chem Soc
Year2001
Volume123
Pages6555-63
AuthorsKaminskaia NV, Spingler B, Lippard SJ
TitleIntermediate in beta-lactam hydrolysis catalyzed by a dinuclear zinc(II) complex: relevance to the mechanism of metallo-beta-lactamase.
[20]
PubMed ID11443136
JournalJ Biol Chem
Year2001
Volume276
Pages33638-44
AuthorsSpencer J, Clarke AR, Walsh TR
TitleNovel mechanism of hydrolysis of therapeutic beta-lactams by Stenotrophomonas maltophilia L1 metallo-beta-lactamase.
[21]
PubMed ID11457108
JournalJ Am Chem Soc
Year2001
Volume123
Pages3759-70
AuthorsSuarez D, Merz KM Jr
TitleMolecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.
[22]
PubMed ID11484222
JournalProteins
Year2001
Volume44
Pages448-59
AuthorsSalsbury FR Jr, Crowley MF, Brooks CL 3rd
TitleModeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding.
[23]
PubMed ID11551939
JournalJ Biol Chem
Year2001
Volume276
Pages45065-78
Authorsde Seny D, Heinz U, Wommer S, Kiefer M, Meyer-Klaucke W, Galleni M, Frere JM, Bauer R, Adolph HW
TitleMetal 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.
[24]
PubMed ID11583551
JournalJ Am Chem Soc
Year2001
Volume123
Pages9867-79
AuthorsDiaz N, Suarez D, Merz KM Jr
TitleMolecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.
[25]
CommentsIdentification of critical residues
PubMed ID11714924
JournalProtein Sci
Year2001
Volume10
Pages2556-65
AuthorsMateron IC, Palzkill T
TitleIdentification of residues critical for metallo-beta-lactamase function by codon randomization and selection.
[26]
CommentsMetal site
PubMed ID11847294
JournalProtein Sci
Year2002
Volume11
Pages707-12
AuthorsGomes CM, Frazao C, Xavier AV, Legall J, Teixeira M
TitleFunctional control of the binuclear metal site in the metallo-beta-lactamase-like fold by subtle amino acid replacements.
[27]
PubMed ID12022865
JournalBiochemistry
Year2002
Volume41
Pages6615-30
AuthorsSuarez D, Brothers EN, Merz KM Jr
TitleInsights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis.
[28]
PubMed ID12203007
JournalJ Biol Inorg Chem
Year2002
Volume7
Pages704-12
AuthorsDal Peraro M, Vila AJ, Carloni P
TitleStructural determinants and hydrogen-bond network of the mononuclear zinc(II)-beta-lactamase active site.
[29]
PubMed ID12395427
JournalJ Comput Chem
Year2002
Volume23
Pages1587-600
AuthorsSuarez D, Diaz N, Merz KM Jr
TitleMolecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem.
[30]
PubMed ID12507470
JournalJ Mol Biol
Year2003
Volume325
Pages651-60
AuthorsGarcia-Saez I, Mercuri PS, Papamicael C, Kahn R, Frere JM, Galleni M, Rossolini GM, Dideberg O
TitleThree-dimensional structure of FEZ-1, a monomeric subclass B3 metallo-beta-lactamase from Fluoribacter gormanii, in native form and in complex with D-captopril.
[31]
PubMed ID12543663
JournalAntimicrob Agents Chemother
Year2003
Volume47
Pages582-7
AuthorsMurphy TA, Simm AM, Toleman MA, Jones RN, Walsh TR
TitleBiochemical characterization of the acquired metallo-beta-lactamase SPM-1 from Pseudomonas aeruginosa.
[32]
PubMed ID12578382
JournalBiochemistry
Year2003
Volume42
Pages1673-83
AuthorsSiemann S, Clarke AJ, Viswanatha T, Dmitrienko GI
TitleThiols as classical and slow-binding inhibitors of IMP-1 and other binuclear metallo-beta-lactamases.
[33]
PubMed ID12611529
JournalInorg Chem
Year2003
Volume42
Pages1604-15
AuthorsBoerzel H, Koeckert M, Bu W, Spingler B, Lippard SJ
TitleZinc-bound thiolate-disulfide exchange: a strategy for inhibiting metallo-beta-lactamases.
[34]
PubMed ID12684522
JournalJ Biol Chem
Year2003
Volume278
Pages23868-73
AuthorsGarcia-Saez I, Hopkins J, Papamicael C, Franceschini N, Amicosante G, Rossolini GM, Galleni M, Frere JM, Dideberg O
TitleThe 1.5-A structure of Chryseobacterium meningosepticum zinc beta-lactamase in complex with the inhibitor, D-captopril.
[35]
PubMed ID12724330
JournalJ Biol Chem
Year2003
Volume278
Pages29240-51
AuthorsDamblon C, Jensen M, Ababou A, Barsukov I, Papamicael C, Schofield CJ, Olsen L, Bauer R, Roberts GC
TitleThe inhibitor thiomandelic acid binds to both metal ions in metallo-beta-lactamase and induces positive cooperativity in metal binding.
[36]
PubMed ID12826725
JournalProtein Eng
Year2003
Volume16
Pages341-50
AuthorsOelschlaeger P, Schmid RD, Pleiss J
TitleInsight into the mechanism of the IMP-1 metallo-beta-lactamase by molecular dynamics simulations.

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).

createdupdated
2002-09-042009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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