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(-) Description

Title :  STRUCTURE-BASED DESIGN OF THE IRREVERSIBLE INHIBITORS TO METALLO--LACTAMASE (IMP-1)
 
Authors :  H. Kurosaki, Y. Yamaguchi, T. Higashi, K. Soga, S. Matsueda, S. Misumi, Y. Yamagata, Y. Arakawa, M. Goto
Date :  27 Apr 04  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metallo-Beta-Lactamase, Zinc, Irreversible Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Kurosaki, Y. Yamaguchi, T. Higashi, K. Soga, S. Matsueda, H. Yumoto, S. Misumi, Y. Yamagata, Y. Arakawa, M. Goto
Irreversible Inhibition Of Metallo-Beta-Lactamase (Imp-1) By 3-(3-Mercaptopropionylsulfanyl)Propionic Acid Pentafluorophenyl Ester
Angew. Chem. Int. Ed. Engl. V. 44 3861 2005
PubMed-ID: 15892033  |  Reference-DOI: 10.1002/ANIE.200500835
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BETA-LACTAMASE IMP-1
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9A-IMP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Synonym: METALLO-BETA-LACTAMASE, BETA-LACTAMASE, TYPE II, PENICILLINASE, BLAIMP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2OPS2Ligand/Ion3-OXO-3-[(3-OXOPROPYL)SULFANYL]PROPANE-1-THIOLATE
3ZN4Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:77 , HIS A:79 , HIS A:139 , OPS A:1161BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREASP A:81 , CYS A:158 , HIS A:197 , OPS A:1161BINDING SITE FOR RESIDUE ZN A 302
3AC3SOFTWAREHIS B:77 , HIS B:79 , HIS B:139 , ZN B:304 , OPS B:1161BINDING SITE FOR RESIDUE ZN B 303
4AC4SOFTWAREASP B:81 , CYS B:158 , HIS B:197 , ZN B:303 , OPS B:1161BINDING SITE FOR RESIDUE ZN B 304
5AC5SOFTWAREHIS A:79 , ASP A:81 , HIS A:139 , LYS A:161 , ASN A:167 , HIS A:197 , ZN A:301 , ZN A:302BINDING SITE FOR RESIDUE OPS A 1161
6AC6SOFTWAREHIS B:79 , ASP B:81 , HIS B:139 , LYS B:161 , ASN B:167 , HIS B:197 , ZN B:303 , ZN B:304BINDING SITE FOR RESIDUE OPS B 1161
7AC7SOFTWAREGLU A:24 , VAL A:25 , GLY A:27 , TRP A:28 , GLY A:29BINDING SITE FOR RESIDUE ACY A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological 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

(-) Exons   (0, 0)

(no "Exon" information available for 1VGN)

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

    Alignment length:217
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       
           BLAB_SERMA    22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 238
               SCOP domains d1vgna_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains 1vgnA00 A:4-220 Metallo-beta-lactamase, chain A                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeee.................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgn A   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 220
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with BLAB_SERMA | P52699 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:218
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        
           BLAB_SERMA    22 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 239
               SCOP domains d1vgnb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains 1vgnB00 B:4-221 Metallo-beta-lactamase, chain A                                                                                                                                                                            CATH domains
           Pfam domains (1) ------------------------Lactamase_B-1vgnB01 B:28-211                                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) ------------------------Lactamase_B-1vgnB02 B:28-211                                                                                                                                                            ---------- Pfam domains (2)
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...ee.hhhhhhhhhhh............eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------BETA_LACTAMASE_B_1  -------------------------------------------------------BETA_LACTAMAS------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vgn B   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESK 221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological 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).

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        BLAB_SERMA | P52699: 1dd6 1jje 1jjt 1wuo 1wup 2doo 4c1f 4c1g 5ev6 5ev8 5ewa 5hh4

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