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(-) Description

Title :  IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH A BIARYL SUCCINIC ACID INHIBITOR (1)
 
Authors :  P. M. D. Fitzgerald, N. Sharma
Date :  09 Jul 01  (Deposition) - 25 Jul 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Metallo-Beta-Lactamase Inhibitor, Succinic Acid Inhibitor, Imp-1 Metallo-Beta-Lactamase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. H. Toney, G. G. Hammond, P. M. Fitzgerald, N. Sharma, J. M. Balkovec, G. P. Rouen, S. H. Olson, M. L. Hammond, M. L. Greenlee, Y. D. Gao
Succinic Acids As Potent Inhibitors Of Plasmid-Borne Imp-1 Metallo-Beta-Lactamase.
J. Biol. Chem. V. 276 31913 2001
PubMed-ID: 11390410  |  Reference-DOI: 10.1074/JBC.M104742200

(-) Compounds

Molecule 1 - IMP-1 METALLO BETA-LACTAMASE
    ChainsA, B
    EC Number3.5.2.6
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentMETALLO-BETA-LACTAMASE
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid287
    Other DetailsPLEASE NOTE THAT THE PROTEIN CONTAINS POSTRANSLATIONAL MODIFICATION: ATOM CG OF ASN 26 IS BOUND TO ATOM N OF GLY 27. THIS ACCOUNTS FOR MISSING ATOMS LISTED IN REMARK 470 AND DISTORTED GEOMETRY REPORTED FOR THESE RESIDUES.

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2BDS2Ligand/Ion2,3-BIS-BENZO[1,3]DIOXOL-5-YLMETHYL-SUCCINIC ACID
3ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BDS1Ligand/Ion2,3-BIS-BENZO[1,3]DIOXOL-5-YLMETHYL-SUCCINIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BDS1Ligand/Ion2,3-BIS-BENZO[1,3]DIOXOL-5-YLMETHYL-SUCCINIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BDS1Ligand/Ion2,3-BIS-BENZO[1,3]DIOXOL-5-YLMETHYL-SUCCINIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:77 , HIS A:79 , HIS A:139 , BDS A:250 , ZN A:252BINDING SITE FOR RESIDUE ZN A 251
02AC2SOFTWAREASP A:81 , CYS A:158 , HIS A:197 , BDS A:250 , ZN A:251BINDING SITE FOR RESIDUE ZN A 252
03AC3SOFTWARELYS A:8 , HIS A:34 , GLU A:199 , ZN A:261 , HOH A:1016BINDING SITE FOR RESIDUE ACT A 260
04AC4SOFTWAREHIS A:34 , GLU A:199 , ACT A:260 , HOH A:1016BINDING SITE FOR RESIDUE ZN A 261
05AC5SOFTWAREHIS B:77 , HIS B:79 , HIS B:139 , BDS B:250 , ZN B:252BINDING SITE FOR RESIDUE ZN B 251
06AC6SOFTWAREASP B:81 , CYS B:158 , HIS B:197 , BDS B:250 , ZN B:251BINDING SITE FOR RESIDUE ZN B 252
07AC7SOFTWARELYS B:8 , HIS B:34 , GLU B:199 , ZN B:261BINDING SITE FOR RESIDUE ACT B 260
08AC8SOFTWAREHIS B:34 , GLU B:199 , ACT B:260BINDING SITE FOR RESIDUE ZN B 261
09AC9SOFTWAREVAL A:25 , TRP A:28 , PHE A:51 , HIS A:77 , HIS A:79 , SER A:80 , ASP A:81 , HIS A:139 , CYS A:158 , LYS A:161 , GLY A:166 , ASN A:167 , HIS A:197 , ZN A:251 , ZN A:252BINDING SITE FOR RESIDUE BDS A 250
10BC1SOFTWAREHIS B:77 , HIS B:79 , SER B:80 , ASP B:81 , HIS B:139 , CYS B:158 , LYS B:161 , GLY B:166 , ASN B:167 , HIS B:197 , ZN B:251 , ZN B:252 , HOH B:1221 , HOH B:1238 , HOH B:1266 , HOH B:1428BINDING SITE FOR RESIDUE BDS B 250

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_SERMA92-111
 
  2A:74-93
B:74-93
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_SERMA167-179
 
  2A:149-161
B:149-161
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_SERMA92-111
 
  1A:74-93
-
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_SERMA167-179
 
  1A:149-161
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_SERMA92-111
 
  1-
B:74-93
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_SERMA167-179
 
  1-
B:149-161
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLAB_SERMA92-111
 
  2A:74-93
B:74-93
2BETA_LACTAMASE_B_2PS00744 Beta-lactamases class B signature 2.BLAB_SERMA167-179
 
  2A:149-161
B:149-161

(-) Exons   (0, 0)

(no "Exon" information available for 1JJT)

(-) 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:220
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
           BLAB_SERMA    21 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKK 240
               SCOP domains d1jjta_ A: Zn metallo-beta-lactamase                                                                                                                                                                                         SCOP domains
               CATH domains 1jjtA00 A:3-222 Metallo-beta-lactamase, chain A                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee.....eee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jjt A   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKK 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain A from PDB  Type:PROTEIN  Length:220
 aligned with Q79MP6_PSEAI | Q79MP6 from UniProtKB/TrEMBL  Length:246

    Alignment length:220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
         Q79MP6_PSEAI    21 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKK 240
               SCOP domains d1jjta_ A: Zn metallo-beta-lactamase                                                                                                                                                                                         SCOP domains
               CATH domains 1jjtA00 A:3-222 Metallo-beta-lactamase, chain A                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee.....eee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jjt A   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKK 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:220
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
           BLAB_SERMA    20 ESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 239
               SCOP domains d1jjtb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                         SCOP domains
               CATH domains 1jjtB00 B:2-221 Metallo-beta-lactamase, chain A                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh....eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jjt B   2 ESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q79MP6_PSEAI | Q79MP6 from UniProtKB/TrEMBL  Length:246

    Alignment length:220
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
         Q79MP6_PSEAI    20 ESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 239
               SCOP domains d1jjtb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                         SCOP domains
               CATH domains 1jjtB00 B:2-221 Metallo-beta-lactamase, chain A                                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeeeee.....eeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh....eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jjt B   2 ESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLAB_SERMA | P52699)
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.
    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.
    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.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Chain A,B   (Q79MP6_PSEAI | Q79MP6)
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.
    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.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        BLAB_SERMA | P526991dd6 1jje 1vgn 1wuo 1wup 2doo 4c1f 4c1g 5ev6 5ev8 5ewa 5hh4
UniProtKB/TrEMBL
        Q79MP6_PSEAI | Q79MP61ddk 1jje 3wxc 4f6h 4f6z

(-) Related Entries Specified in the PDB File

1jje IMP-1 METALLO BETA-LACTAMASE IN COMPLEX WITH 2-BENZO[1,3] DIOXOL-5-YLMETHYL-3-BENZYL-SUCCINIC ACID