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(-) Description

Title :  GIM-1-3MOL NATIVE. 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 :  1.60
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  B  (2x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Hydrolase, Antibiotic Resistance, Residue Determinants, Loop Dynamics (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, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PLYSS PRARE
    Fragment: RESIDUES 19-250
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE GIM-1
 
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
    Fragment: RESIDUES 19-250
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: METALLO-BETA-LACTAMASE GIM-1

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x):  B 
Biological Unit 2 (1x): A C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , ZN A:1297 , HOH A:2140BINDING SITE FOR RESIDUE ZN A1296
2AC2SOFTWAREASP A:120 , CYS A:221 , HIS A:263 , ZN A:1296 , HOH A:2140BINDING SITE FOR RESIDUE ZN A1297
3AC3SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , ZN B:1298 , HOH B:2119BINDING SITE FOR RESIDUE ZN B1297
4AC4SOFTWAREASP B:120 , CYS B:221 , HIS B:263 , ZN B:1297 , HOH B:2119BINDING SITE FOR RESIDUE ZN B1298
5AC5SOFTWAREHIS C:116 , HIS C:118 , HIS C:196 , ZN C:1300 , HOH C:2069BINDING SITE FOR RESIDUE ZN C1299
6AC6SOFTWAREASP C:120 , CYS C:221 , HIS C:263 , ZN C:1299 , HOH C:2069BINDING SITE FOR RESIDUE ZN C1300
7AC7SOFTWAREHIS A:170 , TYR A:171 , ASP C:175 , TYR C:190 , TYR C:191 , GLY C:193 , HOH C:2119 , HOH C:2120BINDING SITE FOR RESIDUE GOL C1301
8AC8SOFTWARELEU A:42 , GLU A:43 , VAL A:44 , TRP A:98 , HOH A:2021 , HOH A:2113 , HOH A:2298 , HOH A:2299 , HOH A:2300 , THR B:169BINDING SITE FOR RESIDUE GOL A1298

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2YNT)

(-) 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:221
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:221
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237 
         Q704V1_PSEAI    18 AQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 238
               SCOP domains d2ynta_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynt A  36 SQGHKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASN 295
                                    45|       56        66        76        86        96   ||| 109       119       129 ||    140       150|      174||     187       197       210||     223       233       243       253       263 ||    284       294 
                                    45|                                                  100||  ||                   131|              150|       175|                       205| ||                                               265|                  
                                     47                                                   102|  ||                    133               165        179                        209 ||                                                277                  
                                                                                           104  ||                                                                              211|                                                                     
                                                                                              107|                                                                               215                                                                     
                                                                                               109                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230         
         Q704V1_PSEAI    21 HKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNK 239
               SCOP domains d2yntb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynt B  39 HKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEALGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNK 296
                                  ||49        59        69        79        89        99|||  ||112       122       133       143      |167       180       190       200    || 216       226       236       246       256       277       287         
                                 45|                                                  100||  ||                   131|              150|       175|                       205| ||                                               265|                   
                                  47                                                   102|  ||                    133               165        179                        209 ||                                                277                   
                                                                                        104  ||                                                                              211|                                                                      
                                                                                           107|                                                                               215                                                                      
                                                                                            109                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:221
 aligned with Q704V1_PSEAI | Q704V1 from UniProtKB/TrEMBL  Length:250

    Alignment length:221
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
         Q704V1_PSEAI    21 HKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLM 241
               SCOP domains d2yntc_ C: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeee....eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh......eeee.......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ynt C  39 HKPLEVIKIEDGVYLHTSFKNIEGYGLVDSNGLVVLDNNQAYIIDTPWSEEDTKLLLSWATDRGYQVMASISTHSHEDRTAGIKLLNSKSIPTYTSELTKKLLAREGKPVPTHYFKDDEFTLGNGLIELYYPGAGHTEDNIVAWLPKSKILFGGCLVRSHEWEGLGYVGDASISSWADSIKNIVSKKYPIQMVVPGHGKVGSSDILDHTIDLAESASNKLM 298
                                  ||49        59        69        79        89        99|||  ||112       122       133       143      |167       180       190       200    || 216       226       236       246       256       277       287       297 
                                 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, 3)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (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: 2ynu 2ynv 2ynw 5acp 5acq 5acr 5acs 5act

(-) Related Entries Specified in the PDB File

2ynu APO GIM-1 WITH 2MOL. CRYSTAL STRUCTURES OF PSEUDOMONAS AERUGINOSA GIM-1: ACTIVE SITE PLASTICITY IN METALLO- BETA-LACTAMASES
2ynv CYS221 OXIDIZED, MONO ZINC GIM-1 - GIM-1-OX. 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