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(-) Description

Title :  CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE SMB-1
 
Authors :  J. Wachino, Y. Yamaguchi, S. Mori, Y. Arakawa, K. Shibayama
Date :  29 Feb 12  (Deposition) - 13 Feb 13  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Wachino, Y. Yamaguchi, S. Mori, H. Kurosaki, Y. Arakawa, K. Shibayama
Structural Insights Into The Subclass B3 Metallo-Beta-Lactamase Smb-1 And The Mode Of Inhibition By The Common Metallo- -Lactamase Inhibitor Mercaptoacetate
Antimicrob. Agents Chemother. V. 57 101 2013
PubMed-ID: 23070156  |  Reference-DOI: 10.1128/AAC.01264-12

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-280
    Gene: BLASMB-1, SMB-1
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Strain: 10MDR148

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:72 , HIS A:74 , HIS A:150 , ZN A:302 , GOL A:309 , HOH A:701 , HOH A:702BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREASP A:76 , HIS A:77 , HIS A:215 , ZN A:301 , GOL A:309 , HOH A:701 , HOH A:702BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWARETHR A:91 , LYS A:125 , HIS A:189 , PRO A:190 , GLU A:191 , VAL A:192 , HOH A:832 , HOH A:913BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:56 , LYS A:61 , LEU A:62 , SER A:63BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREASP A:4 , TRP A:5 , SER A:6 , LYS A:46 , HOH A:902BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREASP A:182 , SER A:183 , VAL A:218 , ASN A:219 , ASP A:220 , ARG A:224 , ALA A:244 , HOH A:793 , HOH A:911BINDING SITE FOR RESIDUE ACT A 306
07AC7SOFTWAREVAL A:179 , SER A:180 , ARG A:256 , HOH A:808 , HOH A:874 , HOH A:968BINDING SITE FOR RESIDUE ACT A 307
08AC8SOFTWARESER A:175 , LEU A:176 , THR A:177 , VAL A:218 , ILE A:245 , GLY A:249 , HOH A:726 , HOH A:766 , HOH A:860BINDING SITE FOR RESIDUE ACT A 308
09AC9SOFTWAREGLN A:113 , HIS A:150 , HIS A:215 , ZN A:301 , ZN A:302 , HOH A:701 , HOH A:709BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREPRO A:108 , LYS A:109 , SER A:110 , LYS A:230BINDING SITE FOR RESIDUE GOL A 310
11BC2SOFTWAREALA A:124 , LYS A:125 , GLU A:152 , HOH A:877 , HOH A:893 , HOH A:971BINDING SITE FOR RESIDUE GOL A 311
12BC3SOFTWARESER A:183 , TYR A:184 , ARG A:185 , ASP A:188 , HIS A:189 , ARG A:227 , GLU A:231 , HOH A:752 , HOH A:947BINDING SITE FOR RESIDUE GOL A 312

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:162 -A:167
2A:208 -A:242

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VPE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VPE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VPE)

(-) Exons   (0, 0)

(no "Exon" information available for 3VPE)

(-) 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:259
 aligned with G5ELM3_SERMA | G5ELM3 from UniProtKB/TrEMBL  Length:280

    Alignment length:259
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270         
         G5ELM3_SERMA    21 RDWSSPQQPFTIYGNTHYVGTGGISAVLLSSPQGHILVDGTTEKGAQVVAANIRAMGFKLSDVKYILSTHSHEDHAGGISAMQKLTGATVLAGAANVDTLRTGVSPKSDPQFGSLSNFPGSAKVRAVADGELVKLGPLAVKAHATPGHTEGGITWTWQSCEQGKCKDVVFADSLTAVSADSYRFSDHPEVVASLRGSFEAVEKLSCDIAIAAHPEVNDMWTRQQRAAKEGNSAYVDNGACRAIAAAGRKRLETRLASEK 279
               SCOP domains d3vpea_ A: automated matches                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..eee........eee.....eeee.....hhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhhh....................eeee....eeee..eeeeeee........eeeeeeeee..eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vpe A   3 RDWSSPQQPFTIYGNTHYVGTGGISAVLLSSPQGHILVDGTTEKGAQVVAANIRAMGFKLSDVKYILSTHSHEDHAGGISAMQKLTGATVLAGAANVDTLRTGVSPKSDPQFGSLSNFPGSAKVRAVADGELVKLGPLAVKAHATPGHTEGGITWTWQSCEQGKCKDVVFADSLTAVSADSYRFSDHPEVVASLRGSFEAVEKLSCDIAIAAHPEVNDMWTRQQRAAKEGNSAYVDNGACRAIAAAGRKRLETRLASEK 261
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   Legend:   → Mismatch (orange background)
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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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VPE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VPE)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (G5ELM3_SERMA | G5ELM3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        G5ELM3_SERMA | G5ELM3: 3vqz 5axo 5axr 5aya 5b15 5b1u

(-) Related Entries Specified in the PDB File

3vqz