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(-) Description

Title :  CRYSTAL STRUCTURE OF A HALOTOLERANT BACTERIAL BETA-LACTAMASE
 
Authors :  C. A. Smith, S. B. Vakulenko
Date :  15 Jan 10  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Beta-Lactamase, Antibiotic Resistance, Halotolerant, Deep- Sea Bacterium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Toth, C. Smith, H. Frase, S. Mobashery, S. Vakulenko
An Antibiotic-Resistance Enzyme From A Deep-Sea Bacterium
J. Am. Chem. Soc. V. 132 816 2010
PubMed-ID: 20000704  |  Reference-DOI: 10.1021/JA908850P

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: MATURE BETA-LACTAMASE
    Gene: OB2793, OIH-1
    Organism Scientific: OCEANOBACILLUS IHEYENSIS
    Organism Taxid: 182710

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECA A:2 , CA A:3 , ASP A:159 , GLU A:162 , GLU A:174 , MET A:175 , ASP A:176 , ASP A:213BINDING SITE FOR RESIDUE CA A 1
02AC2SOFTWARECA A:1 , ASP A:159 , ASP A:176 , ASP A:213 , HOH A:516 , HOH A:517 , HOH A:518 , HOH A:519BINDING SITE FOR RESIDUE CA A 2
03AC3SOFTWARECA A:1 , GLU A:162 , GLU A:174 , ASP A:213 , HOH A:520 , HOH A:521 , HOH A:522BINDING SITE FOR RESIDUE CA A 3
04AC4SOFTWARETHR A:67 , ASP A:70 , HOH A:523BINDING SITE FOR RESIDUE CA A 4
05AC5SOFTWAREHOH A:9 , HOH A:10 , HOH A:11 , HOH A:12 , HOH A:13BINDING SITE FOR RESIDUE CA A 5
06AC6SOFTWAREHOH A:14 , HOH A:15 , HOH A:16 , SER A:74 , GLU A:77BINDING SITE FOR RESIDUE CA A 6
07AC7SOFTWAREHOH A:17 , HOH A:18 , HOH A:19 , HOH A:21 , HOH A:22 , GLY A:169 , HOH A:524BINDING SITE FOR RESIDUE CA A 7
08AC8SOFTWAREHOH A:23 , HOH A:24 , HOH A:25 , HOH A:26 , ASP A:101 , ASP A:215 , HOH A:520BINDING SITE FOR RESIDUE CA A 8
09AC9SOFTWAREPRO A:158 , ASP A:159 , HOH A:517 , HOH A:535BINDING SITE FOR RESIDUE CL A 20
10BC1SOFTWARESER A:85 , TYR A:118 , SER A:143 , THR A:228 , ASP A:231 , LYS A:247 , THR A:248 , GLY A:249 , ARG A:256 , HOH A:528 , HOH A:562 , HOH A:706BINDING SITE FOR RESIDUE EPE A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LEZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:179 -Thr A:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LEZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LEZ)

(-) Exons   (0, 0)

(no "Exon" information available for 3LEZ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:260
 aligned with Q8EMP8_OCEIH | Q8EMP8 from UniProtKB/TrEMBL  Length:304

    Alignment length:260
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304
         Q8EMP8_OCEIH    45 GSEDLKKLEEEFDVRLGVYAIDTGADKEISYRENERFAYTSTFKPLAVGAVLQTKSDEELEETITYSEEDLVTYSPITEQHVDEGMTLVEIADAAIRYSDNTAGNLLLEAMGGPDELETILRDIGDETIEMDRYETELNEAKPGDIRDTSTAKAMATTLQQYVLEDVLDADRREVLTNMLINNTTGDALIRAGVPDGWTVGDKTGAGGYGTRNDIGIIWPEGDEEPIVIAIMSSRDEEDADYDDKLIEKATEIVLQELRN 304
               SCOP domains d3leza_ A: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3lezA00 A:45-304 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------Beta-lactamase2-3lezA01 A:66-275                                                                                                                                                                                  ----------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.eeeeeeee....eeeee....eee.hhhhhhhhhhhhhhhhhhhhhhhee..hhhhh.....hhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...........hhhhh........eeehhhhhhhhhhhhh....hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeee.......eeeeeeee.........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lez A  45 GSEDLKKLEEEFDVRLGVYAIDTGADKEISYRENERFAYTSTFKPLAVGAVLQTKSDEELEETITYSEEDLVTYSPITEQHVDEGMTLVEIADAAIRYSDNTAGNLLLEAMGGPDELETILRDIGDETIEMDRYETELNEAKPGDIRDTSTAKAMATTLQQYVLEDVLDADRREVLTNMLINNTTGDALIRAGVPDGWTVGDKTGAGGYGTRNDIGIIWPEGDEEPIVIAIMSSRDEEDADYDDKLIEKATEIVLQELRN 304
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q8EMP8_OCEIH | Q8EMP8)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0030655    beta-lactam antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a beta-lactam antibiotic, any member of a class of natural or semisynthetic antibiotics whose characteristic feature is a strained, four-membered beta-lactam ring. They include the penicillins and many of the cephalosporins.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

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