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(-) Description

Title :  VIM-7 WITH OXIDISED. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF VIM-7: INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA-LACTAMASES
 
Authors :  P. Saradhi, H. -K. S. Leiros, R. Ahmad, J. Spencer, I. Leiros, T. R. Walsh A. Sundsfjord, O. Samuelsen
Date :  03 Feb 11  (Deposition) - 15 Jun 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.33
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Keywords :  Hydrolase, Cephalosporins, Antibiotic Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Saradhi, H. -K. S. Leiros, R. Ahmad, J. Spencer, I. Leiros, T. R. Walsh, A. Sundsfjord, O. Samuelsen
Structural And Computational Investigations Of Vim- 7: Insights Into The Substrate Specificity Of Vim Metallo-Beta-Lactamases
J. Mol. Biol. V. 411 174 2011
PubMed-ID: 21645522  |  Reference-DOI: 10.1016/J.JMB.2011.05.035

(-) Compounds

Molecule 1 - METALLO-B-LACTAMASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE VIM-7, METALLO-BETA-LACTAMASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2UNX1Ligand/IonUNKNOWN ATOM OR ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2UNX1Ligand/IonUNKNOWN ATOM OR ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196BINDING SITE FOR RESIDUE ZN A1292
2AC2SOFTWAREASP A:120 , CYS A:221 , HIS A:263BINDING SITE FOR RESIDUE ZN A1293
3AC3SOFTWAREASP A:119 , ASN A:165 , HOH A:2033 , HOH A:2034 , HOH A:2040BINDING SITE FOR RESIDUE MG A1294

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y8A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y8A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y8A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y8A)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y8A)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:226
 aligned with Q840P9_PSEAI | Q840P9 from UniProtKB/TrEMBL  Length:265

    Alignment length:226
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250      
         Q840P9_PSEAI    31 EYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTVALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYTSPLTRQLAEAAGNEVPAHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGNVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTNVVK 256
               SCOP domains d2y8aa_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh....eeeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhh......ee........eeeee..eeeee..........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y8a A  30 EYPTVDDIPVGEVRLYKIGDGVWSHIATQKLGDTVYSSNGLIVRDADELLLIDTAWGAKNTVALLAEIEKQIGLPVTRSISTHFHDDRVGGVDVLRAAGVATYTSPLTRQLAEAAGNEVPAHSLKALSSSGDVVRFGPVEVFYPGAAHSGDNLVVYVPAVRVLFGGCAVHEASRESAGNVADANLAEWPATIKRIQQRYPEAEVVIPGHGLPGGLELLQHTTNVVK 291
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285      
                                          45|               64|                               100|  107|                   131|              150|                                     205| ||                                               265|              
                                           47                66                                102   109                    133               165                                      209 ||                                                277              
                                                                                                                                                                                         211|                                                                 
                                                                                                                                                                                          215
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  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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y8A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y8A)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q840P9_PSEAI | Q840P9)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q840P9_PSEAI | Q840P9: 2y87 2y8b 4d1t 4d1u 4d1v 4d1w

(-) Related Entries Specified in the PDB File

2y87 NATIVE VIM-7. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF VIM-7: INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA-LACTAMASES
2y8b VIM-7 WITH OXIDISED. STRUCTURAL AND COMPUTATIONAL INVESTIGATIONS OF VIM-7: INSIGHTS INTO THE SUBSTRATE SPECIFICITY OF VIM METALLO-BETA-LACTAMASES