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(-) Description

Title :  VIM-2, A ZN-BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA WITH CYS221 REDUCED
 
Authors :  I. Garcia-Saez, J. -D. Docquier, G. M. Rossolini, O. Dideberg
Date :  20 Dec 01  (Deposition) - 02 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta/Beta-Alpha Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Garcia-Saez, J. -D. Docquier, G. M. Rossolini, O. Dideberg
The Three-Dimensional Structure Of Vim-2, A Zn-Beta-Lactamase From Pseudomonas Aeruginosa In Its Reduced And Oxidised Form
J. Mol. Biol. V. 375 604 2008
PubMed-ID: 18061205  |  Reference-DOI: 10.1016/J.JMB.2007.11.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VIM-2 METALLO-BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9-VIM-2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 30-295
    Gene: BLAVIM-2
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3OH1Ligand/IonHYDROXIDE ION
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , OH A:1001 , HOH A:1108BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , CL A:402 , OH A:1001BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREHIS A:170 , HIS A:285 , ACT A:400 , ACT A:401BINDING SITE FOR RESIDUE ZN A 3
4AC4SOFTWAREZN A:3 , ALA A:135 , THR A:136 , THR A:169 , HIS A:170 , HIS A:285 , ACT A:401 , HOH A:1010BINDING SITE FOR RESIDUE ACT A 400
5AC5SOFTWAREZN A:3 , ALA A:135 , HIS A:170 , HIS A:285 , ASN A:288 , ACT A:400 , HOH A:1082BINDING SITE FOR RESIDUE ACT A 401
6AC6SOFTWAREZN A:2 , OH A:1001 , HOH A:1002BINDING SITE FOR RESIDUE CL A 402
7AC7SOFTWAREZN A:1 , ZN A:2 , HIS A:116 , HIS A:118 , ASP A:120 , HIS A:196 , CYS A:221 , CL A:402 , HOH A:1108BINDING SITE FOR RESIDUE OH A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KO3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KO3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KO3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KO3)

(-) Exons   (0, 0)

(no "Exon" information available for 1KO3)

(-) Sequences/Alignments

Asymmetric/Biological 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:230
 aligned with Q9K2N0_PSEAI | Q9K2N0 from UniProtKB/TrEMBL  Length:266

    Alignment length:230
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
         Q9K2N0_PSEAI    32 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTN 261
               SCOP domains d1ko3a_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                   SCOP domains
               CATH domains 1ko3A00 A:30-295 Metallo-beta-lactamase, chain A                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee..eeeeeeeeee..eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhh..eeeehhhhhhhhhhhh.....ee.........eeee..eeee...........eeee....eeeeehhh.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ko3 A  30 EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTN 295
                                    39     || 50        60   ||   71        81        91       102    || 113       123       134       144     ||168       178       188       198      |211|      224       234       244       254       264||     285       295
                                          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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KO3)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9K2N0_PSEAI | Q9K2N0)
molecular function
    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.

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  3.5.2.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q9K2N0_PSEAI | Q9K2N0: 5k48 5n4s 5n4t 5nhz 5ni0
UniProtKB/TrEMBL
        Q9K2N0_PSEAI | Q9K2N0: 1ko2 4bz3 4c1d 4c1e 4nq2 4pvo 4pvt 4ua4 5acu 5acv 5acw 5acx 5fqc 5lca 5lcf 5lch 5le1 5lm6

(-) Related Entries Specified in the PDB File

1ko2 1KO2 CONTAINS THE SAME PROTEIN(WITH AN OXIDIZED CYS221)