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(-) Description

Title :  CYS221 OXIDIZED, MONO ZINC GIM-1 - GIM-1-OX. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO-BETA-LACTAMASES
 
Authors :  P. S. Borra, O. Samuelsen, J. Spencer, M. S. Lorentzen, H. -K. S. Leiros
Date :  18 Oct 12  (Deposition) - 24 Jul 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. S. Borra, O. Samuelsen, J. Spencer, T. R. Walsh, M. S. Lorentzen, H. -K. S. Leiros
Crystal Structures Of Pseudomonas Aeruginosa Gim-1: Active- Site Plasticity In Metallo-Beta-Lactamases.
Antimicrob. Agents Chemother. V. 57 848 2013
PubMed-ID: 23208706  |  Reference-DOI: 10.1128/AAC.02227-12

(-) Compounds

Molecule 1 - GIM-1 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PLYSS PRARE
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE GIM-1, METALLO-BETA-LACTAMASE
 
Molecule 2 - GIM-1 PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PLYSS PRARE
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE GIM-1, METALLO-BETA-LACTAMASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196BINDING SITE FOR RESIDUE ZN A1296
2AC2SOFTWAREHIS A:55 , SER A:57 , SER A:69 , PRO A:86 , HOH A:2005BINDING SITE FOR RESIDUE MG A1297
3AC3SOFTWAREHIS B:116 , HIS B:118 , HIS B:196BINDING SITE FOR RESIDUE ZN B1296

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YNV)

(-) 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:217
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q704V1_PSEAI    22 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 238
               SCOP domains d2ynva_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhh....eeeehhhhhhhhhh......eee...eeeehhhheeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynv A  40 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGcLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 295
                                 || 50        60        70        80        90       100||  || 113       123       134       144     ||168      |181       191       201   || |217   |   227       237       247       257       278       288       
                                45|                                                  100||  ||                   131|              150|       175|                       205| ||     |                                         265|                  
                                 47                                                   102|  ||                    133               165        179                        209 ||     |                                          277                  
                                                                                       104  ||                                                                              211|     |                                                               
                                                                                          107|                                                                               215     |                                                               
                                                                                           109                                                                                     221-OCS                                                           


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
         Q704V1_PSEAI    22 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 238
               SCOP domains d2ynvb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeeeeeee..eeeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhh...eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynv B  40 KPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 295
                                 || 50        60        70        80        90       100||  || 113       123       134       144     ||168      |181       191       201   || |217       227       237       247       257       278       288       
                                45|                                                  100||  ||                   131|              150|       175|                       205| ||                                               265|                  
                                 47                                                   102|  ||                    133               165        179                        209 ||                                                277                  
                                                                                       104  ||                                                                              211|                                                                     
                                                                                          107|                                                                               215                                                                     
                                                                                           109
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  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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q704V1_PSEAI | Q704V1)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q704V1_PSEAI | Q704V1: 2ynt 2ynu 2ynw 5acp 5acq 5acr 5acs 5act

(-) Related Entries Specified in the PDB File

2ynt GIM-1-3MOL NATIVE. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES
2ynu APO GIM-1 WITH 2MOL. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES
2ynw GIM-1-2MOL NATIVE. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES