DB code: S00512

RLCP classification 1.13.30000.16 : Hydrolysis
CATH domain 3.40.710.10 : Beta-lactamase Catalytic domain
E.C. 3.5.2.6
CSA 2blt
M-CSA 2blt
MACiE

CATH domain Related DB codes (homologues)
3.40.710.10 : Beta-lactamase S00513 S00529 S00414 T00222

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam RefSeq
P05364 Beta-lactamase
EC 3.5.2.6
Cephalosporinase
S12.006 (Serine)
PF00144 (Beta-lactamase)
[Graphical View]
P00811 Beta-lactamase
EC 3.5.2.6
Cephalosporinase
S12.006 (Serine)
PF00144 (Beta-lactamase)
[Graphical View] 		NP_418574.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_492295.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
Q46041
Beta-lactamase
PF00144 (Beta-lactamase)
[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
P05364 AMPC_ENTCL A beta-lactam + H(2)O = a substituted beta- amino acid. Periplasm (By similarity).
P00811 AMPC_ECOLI A beta-lactam + H(2)O = a substituted beta- amino acid. Monomer. Periplasm.
Q46041 Q46041_CITFR

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

Compound table
Substrates Products Intermediates
KEGG-id C01866 C00395 C00875 C00001 C03806
E.C.
Compound beta-Lactam Penicillin Cephalosporin H2O Substituted beta-amino acid
Type amide group amide group,carboxyl group,sulfide group amide group,amine group,carboxyl group,sulfide group H2O amino acids
ChEBI 15377
 15377
PubChem 22247451
 962
 22247451
 962
1blsA Unbound Unbound Unbound Unbound Transition-state-analogue:IPP
1blsB Unbound Unbound Unbound Unbound Transition-state-analogue:IPP
1gceA Unbound Unbound Unbound Unbound Unbound
1c3bA Unbound Unbound Unbound Unbound Transition-state-analogue:BZB
1c3bB Unbound Unbound Unbound Unbound Transition-state-analogue:BZB
1fcmA Unbound Unbound Unbound Unbound Intermediate-analogue:CXN
1fcmB Unbound Unbound Unbound Unbound Intermediate-analogue:CXN
1fcnA Unbound Unbound Unbound Unbound Intermediate-analogue:LOR
1fcnB Unbound Unbound Unbound Unbound Intermediate-analogue:LOR
1fcoA Unbound Unbound Unbound Unbound Intermediate-analogue:MOX
1fcoB Unbound Unbound Unbound Unbound Intermediate-analogue:MOX
1fswA Unbound Unbound Unbound Unbound Transition-state-analogue:CTB
1fswB Unbound Unbound Unbound Unbound Transition-state-analogue:CTB
1fsyA Unbound Unbound Unbound Unbound Transition-state-analogue:105
1fsyB Unbound Unbound Unbound Unbound Transition-state-analogue:105
2blsA Unbound Unbound Unbound Unbound Unbound
2blsB Unbound Unbound Unbound Unbound Unbound
2bltA Unbound Unbound Unbound Unbound Unbound
2bltB Unbound Unbound Unbound Unbound Unbound
3blsA Unbound Unbound Unbound Unbound Transition-state-analogue:APB
3blsB Unbound Unbound Unbound Unbound Transition-state-analogue:APB
1fr1A Unbound Unbound Unbound Unbound Unbound
1fr1B Unbound Unbound Unbound Unbound Unbound
1fr6A Unbound Unbound Unbound Unbound Intermediate-analogue:AZR
1fr6B Unbound Unbound Unbound Unbound Intermediate-analogue:AZR

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
1blsA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
1blsB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
1gceA SER 64;LYS 67;TYR 150;LYS 318;THR 319 SER 64;SER 321
1c3bA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1c3bB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1fcmA SER 61;LYS 64; ;LYS 312;THR 313 SER 61;ALA 315 mutant Q117L, Y147E
1fcmB SER 61;LYS 64; ;LYS 312;THR 313 SER 61;ALA 315 mutant Q117L, Y147E
1fcnA SER 61;LYS 64; ;LYS 312;THR 313 SER 61;ALA 315 mutant Q117L, Y147E
1fcnB SER 61;LYS 64; ;LYS 312;THR 313 SER 61;ALA 315 mutant Q117L, Y147E
1fcoA SER 61;LYS 64;TYR 147;LYS 312;THR 313 SER 61;ALA 315
1fcoB SER 61;LYS 64;TYR 147;LYS 312;THR 313 SER 61;ALA 315
1fswA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1fswB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1fsyA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1fsyB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
2blsA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
2blsB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
2bltA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
2bltB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
3blsA SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
3blsB SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;ALA 318
1fr1A SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
1fr1B SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
1fr6A SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318
1fr6B SER 64;LYS 67;TYR 150;LYS 315;THR 316 SER 64;SER 318

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.3 3
[2]
p.11261
[4]
p.6767-6771
[5]
Fig.7, p.8584-8586 2
[11]
p.2334-2336
[12]
Fig.1, p.10511-10512
[14]
Fig.2 2
[15]
p.4619-4620
[17]
p.6238-6239
[22]
Fig.1(A), Fig.5, p.418-419, p.421 2
[26]
p.180
[29]
p.1768-1769

References
[1]
Resource
Comments X-ray crystallography (2.0 Angstroms)
Medline ID
PubMed ID 2300174
Journal Nature
Year 1990
Volume 343
Pages 284-8
Authors Oefner C, D'Arcy A, Daly JJ, Gubernator K, Charnas RL, Heinze I, Hubschwerlen C, Winkler FK
Title Refined crystal structure of beta-lactamase from Citrobacter freundii indicates a mechanism for beta-lactam hydrolysis.
Related PDB 1fr1 1fr6
Related UniProtKB
[2]
Resource
Comments X-ray crystallography (2 Angstroms)
Medline ID 94068583
PubMed ID 8248237
Journal Proc Natl Acad Sci U S A
Year 1993
Volume 90
Pages 11257-61
Authors Lobkovsky E, Moews PC, Liu H, Zhao H, Frere JM, Knox JR
Title Evolution of an enzyme activity: crystallographic structure at 2-A resolution of cephalosporinase from the ampC gene of Enterobacter cloacae P99 and comparison with a class A penicillinase.
Related PDB 2blt
Related UniProtKB P05364
[3]
Resource
Comments
Medline ID
PubMed ID 8172894
Journal Biochemistry
Year 1994
Volume 33
Pages 5193-201
Authors Monnaie D, Dubus A, Cooke D, Marchand-Brynaert J, Normark S, Frere JM
Title Role of residue Lys315 in the mechanism of action of the Enterobacter cloacae 908R beta-lactamase.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-ray crystallography (2.3 Angstroms)
Medline ID 94263990
PubMed ID 8204611
Journal Biochemistry
Year 1994
Volume 33
Pages 6762-72
Authors Lobkovsky E, Billings EM, Moews PC, Rahil J, Pratt RF, Knox JR
Title Crystallographic structure of a phosphonate derivative of the Enterobacter cloacae P99 cephalosporinase: mechanistic interpretation of a beta-lactamase transition-state analog.
Related PDB 1bls
Related UniProtKB P05364
[5]
Resource
Comments
Medline ID
PubMed ID 8031792
Journal Biochemistry
Year 1994
Volume 33
Pages 8577-86
Authors Dubus A, Normark S, Kania M, Page MG
Title The role of tyrosine 150 in catalysis of beta-lactam hydrolysis by AmpC beta-lactamase from Escherichia coli investigated by site-directed mutagenesis.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-ray crystallography (2.0-2.3 Angstroms)
Medline ID 99036630
PubMed ID 9819201
Journal Biochemistry
Year 1998
Volume 37
Pages 16082-92
Authors Usher KC, Blaszczak LC, Weston GS, Shoichet BK, Remington SJ
Title Three-dimensional structure of AmpC beta-lactamase from Escherichia coli bound to a transition-state analogue: possible implications for the oxyanion hypothesis and for inhibitor design.
Related PDB 2bls
Related UniProtKB P00811
[7]
Resource
Comments
Medline ID
PubMed ID 9931012
Journal Biochemistry
Year 1999
Volume 38
Pages 1469-77
Authors Adediran SA, Pratt RF
Title Beta-secondary and solvent deuterium kinetic isotope effects on catalysis by the Streptomyces R61 DD-peptidase: comparisons with a structurally similar class C beta-lactamase.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 10049265
Journal Antimicrob Agents Chemother
Year 1999
Volume 43
Pages 543-8
Authors Trepanier S, Knox JR, Clairoux N, Sanschagrin F, Levesque RC, Huletsky A
Title Structure-function studies of Ser-289 in the class C beta-lactamase from Enterobacter cloacae P99.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 10393100
Journal Biochem J
Year 1999
Volume 341
Pages 409-13
Authors Rhazi N, Galleni M, Page MI, Frere JM
Title Peptidase activity of beta-lactamases.
Related PDB
Related UniProtKB
[10]
Resource
Comments X-ray crystallography (1.8 Angstroms)
Medline ID
PubMed ID 10441119
Journal Biochemistry
Year 1999
Volume 38
Pages 10256-61
Authors Crichlow GV, Kuzin AP, Nukaga M, Mayama K, Sawai T, Knox JR
Title Structure of the extended-spectrum class C beta-lactamase of Enterobacter cloacae GC1, a natural mutant with a tandem tripeptide insertion.
Related PDB 1gce
Related UniProtKB
[11]
Resource
Comments X-ray crystallography (2.25 Angstroms)
Medline ID 20060984
PubMed ID 10595535
Journal Protein Sci
Year 1999
Volume 8
Pages 2330-2337
Authors Powers RA, Blazquez J, Weston GS, Morosini MI, Baquero F, Shoichet BK
Title The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
Related PDB 1c3b
Related UniProtKB P00811
[12]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 2000
Volume 122
Pages 10504-12
Authors Patera A, Blaszczak LC, Shoichet BK
Title Crystal structures of substrate and inhibitor complexes with ampc -lactamase: possible implications for substrate-assisted catalysis.
Related PDB 1fcm 1fcn 1fco
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11134945
Journal Acta Crystallogr D Biol Crystallogr
Year 2001
Volume 57
Pages 162-4
Authors Wouters J, Charlier P, Monnaie D, Frere JM, Fonze E
Title Expression, purification, crystallization and preliminary X-ray analysis of the native class C beta-lactamase from Enterobacter cloacae 908R and two mutants.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-ray crystallography (1.75/1.90 Angstroms)
Medline ID
PubMed ID 11182316
Journal Chem Biol
Year 2001
Volume 8
Pages 17-31
Authors Caselli E, Powers RA, Blasczcak LC, Wu CY, Prati F, Shoichet BK
Title Energetic, structural, and antimicrobial analyses of beta-lactam side chain recognition by beta-lactamases.
Related PDB 1fsw 1fsy
Related UniProtKB
[15]
Resource
Comments
Medline ID
PubMed ID 11294628
Journal Biochemistry
Year 2001
Volume 40
Pages 4610-21
Authors Kaur K, Pratt RF
Title Mechanism of reaction of acyl phosph(on)ates with the beta-lactamase of Enterobacter cloacae P99.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 11300697
Journal Bioorg Chem
Year 2001
Volume 29
Pages 77-95
Authors Slater MJ, Laws AP, Page MI
Title The relative catalytic efficiency of beta-lactamase catalyzed acyl and phosphyl transfer.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 11371184
Journal Biochemistry
Year 2001
Volume 40
Pages 6233-9
Authors Crichlow GV, Nukaga M, Doppalapudi VR, Buynak JD, Knox JR
Title Inhibition of class C beta-lactamases: structure of a reaction intermediate with a cephem sulfone.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 11434768
Journal Biochemistry
Year 2001
Volume 40
Pages 7992-9
Authors Trehan I, Beadle BM, Shoichet BK
Title Inhibition of AmpC beta-lactamase through a destabilizing interaction in the active site.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 11478888
Journal Biochemistry
Year 2001
Volume 40
Pages 9207-14
Authors Powers RA, Caselli E, Focia PJ, Prati F, Shoichet BK
Title Structures of ceftazidime and its transition-state analogue in complex with AmpC beta-lactamase: implications for resistance mutations and inhibitor design.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 11709298
Journal Antimicrob Agents Chemother
Year 2001
Volume 45
Pages 3279-86
Authors Rudgers GW, Huang W, Palzkill T
Title Binding properties of a peptide derived from beta-lactamase inhibitory protein.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 11914079
Journal Biochemistry
Year 2002
Volume 41
Pages 4329-38
Authors Bell JH, Pratt RF
Title Mechanism of inhibition of the beta-lactamase of Enterobacter cloacae P99 by 1:1 complexes of vanadate with hydroxamic acids.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 12005439
Journal Structure (Camb)
Year 2002
Volume 10
Pages 413-24
Authors Beadle BM, Trehan I, Focia PJ, Shoichet BK
Title Structural milestones in the reaction pathway of an amide hydrolase: substrate, acyl, and product complexes of cephalothin with AmpC beta-lactamase.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 12121656
Journal Structure (Camb)
Year 2002
Volume 10
Pages 1013-23
Authors Powers RA, Morandi F, Shoichet BK
Title Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 12435704
Journal Antimicrob Agents Chemother
Year 2002
Volume 46
Pages 3978-80
Authors Beadle BM, Shoichet BK
Title Structural basis for imipenem inhibition of class C beta-lactamases.
Related PDB
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 12482929
Journal Proc Natl Acad Sci U S A
Year 2002
Volume 99
Pages 16537-42
Authors Baker K, Bleczinski C, Lin H, Salazar-Jimenez G, Sengupta D, Krane S, Cornish VW
Title Chemical complementation: a reaction-independent genetic assay for enzyme catalysis.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 12513696
Journal Biochem J
Year 2003
Volume 371
Pages 175-81
Authors Kato-Toma Y, Iwashita T, Masuda K, Oyama Y, Ishiguro M
Title pKa measurements from nuclear magnetic resonance of tyrosine-150 in class C beta-lactamase.
Related PDB
Related UniProtKB
[27]
Resource
Comments
Medline ID
PubMed ID 12696055
Journal Proteins
Year 2003
Volume 51
Pages 442-52
Authors Fenollar-Ferrer C, Frau J, Donoso J, Munoz F
Title Role of beta-lactam carboxyl group on binding of penicillins and cephalosporins to class C beta-lactamases.
Related PDB
Related UniProtKB
[28]
Resource
Comments
Medline ID
PubMed ID 12904027
Journal J Am Chem Soc
Year 2003
Volume 125
Pages 9612-8
Authors Meroueh SO, Minasov G, Lee W, Shoichet BK, Mobashery S
Title Structural aspects for evolution of beta-lactamases from penicillin-binding proteins.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 14521155
Journal Cell Mol Life Sci
Year 2003
Volume 60
Pages 1764-73
Authors Wouters J, Fonze E, Vermeire M, Frere JM, Charlier P
Title Crystal structure of Enterobacter cloacae 908R class C beta-lactamase bound to iodo-acetamido-phenyl boronic acid, a transition-state analogue.
Related PDB
Related UniProtKB

Comments
This enzyme belongs to the class-C beta-lactamase family.
Ser64 acts as a nucleophile, making a nucleophilic attack on beta-lactam ring, to form acyl-enzyme intermediate.
According to the early studies ([1], [3], [4] & [5]), Tyr150 was considered to function as general acid-base.
In contrast, the more recent report, [22], suggested substrate-assisted base. In this reported mechanism, C4' carboxylate of the substrate may activate Tyr150, which in turn may activate Ser64 by abstracting a proton from the serine residue during the acylation step [22]. Lys67 might play an intermediary role in transfer of the proton [22].
In the next deacylation step, a water molecule bound to Thr316 (and possibly Tyr150) makes an attack on the C8 carbonyl carbon of the acyl-enzyme intermediate, activating the Ser64 to be a leaving group [22].
The role of Tyr150 seems to be still controversial. However, considering the structure with ligand, Ser64, Tyr150, and Lys150 act as a nucleophile, acid-base, and a modulator for acid-base. Here, mainchain amide groups of Ser64 and Ser318 form an oxyanion hole. These suggest that the mechanism is very similar to that of trypsin (D00197).

Created Updated
2002-09-27 2009-10-01