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(-) Description

Title :  CRYSTAL STRUCTURE OF CLASS C BETA-LACTAMASE MOX-1
 
Authors :  A. Shimizu-Ibuka, T. Oguri, T. Furuyama, Y. Ishii
Date :  15 Mar 13  (Deposition) - 23 Apr 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Lactamase, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Oguri, T. Furuyama, T. Okuno, Y. Ishii, K. Tateda, R. A. Bonomo, A. Shimizu-Ibuka
Crystal Structure Of Mox-1, A Unique Plasmid-Mediated Class C Beta-Lactamase With Hydrolytic Activity Towards Moxalacta
Antimicrob. Agents Chemother. V. 58 3914 2014
PubMed-ID: 24777102  |  Reference-DOI: 10.1128/AAC.02363-13

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 24-382
    Gene: BLAMOX-1
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2SEP1Mod. Amino AcidPHOSPHOSERINE
3ZN11Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:161 , ACT A:1013 , ACT A:1014 , HOH A:3176BINDING SITE FOR RESIDUE ZN A 1001
02AC2SOFTWAREHIS A:24 , ACT A:1012 , HOH A:3004BINDING SITE FOR RESIDUE ZN A 1002
03AC3SOFTWAREHIS A:259 , HOH A:3041 , HOH A:3084BINDING SITE FOR RESIDUE ZN A 1003
04AC4SOFTWAREVAL A:278 , HIS A:351 , ACT A:1015 , HOH A:3070BINDING SITE FOR RESIDUE ZN A 1004
05AC5SOFTWAREGLU A:50 , HIS A:148 , HOH A:3310BINDING SITE FOR RESIDUE ZN A 1005
06AC6SOFTWAREHIS A:186 , ACT A:1016 , HOH A:3126BINDING SITE FOR RESIDUE ZN A 1006
07AC7SOFTWAREHIS A:256 , HOH A:3173 , HOH A:3260BINDING SITE FOR RESIDUE ZN A 1007
08AC8SOFTWAREASP A:14 , HOH A:3247 , HOH A:3248BINDING SITE FOR RESIDUE ZN A 1008
09AC9SOFTWAREASP A:220BINDING SITE FOR RESIDUE ZN A 1009
10BC1SOFTWAREHIS A:187 , ASP A:231 , HOH A:3063 , HOH A:3092 , HOH A:3124 , HOH A:3196BINDING SITE FOR RESIDUE ZN A 1010
11BC2SOFTWAREASP A:7 , HIS A:40 , HOH A:3149BINDING SITE FOR RESIDUE ZN A 1011
12BC3SOFTWAREGLU A:23 , HIS A:24 , ZN A:1002 , HOH A:3131BINDING SITE FOR RESIDUE ACT A 1012
13BC4SOFTWARESER A:129 , MET A:132 , ARG A:133 , HIS A:161 , ZN A:1001 , ACT A:1014BINDING SITE FOR RESIDUE ACT A 1013
14BC5SOFTWAREHIS A:93 , TRP A:96 , HIS A:161 , SER A:165 , ZN A:1001 , ACT A:1013 , HOH A:3033BINDING SITE FOR RESIDUE ACT A 1014
15BC6SOFTWARETYR A:276 , PRO A:277 , VAL A:278 , HIS A:351 , ZN A:1004 , HOH A:3036 , HOH A:3070BINDING SITE FOR RESIDUE ACT A 1015
16BC7SOFTWAREHIS A:186 , ZN A:1006 , HOH A:3005BINDING SITE FOR RESIDUE ACT A 1016

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W8K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:276 -Pro A:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W8K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W8K)

(-) Exons   (0, 0)

(no "Exon" information available for 3W8K)

(-) 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:347
 aligned with Q51578_KLEPN | Q51578 from UniProtKB/TrEMBL  Length:382

    Alignment length:353
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379   
         Q51578_KLEPN    30 DPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGSVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRVNPGMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPRESGSQVLFNKTGSSNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG 382
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeeeeeee..eeeeeeeeeee....ee......ee...hhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhh.hhhhhhh...............hhhhhhhhhhhh........ee..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.........hhhhhhhh..ee.....ee..--..hhhhhhh.eehhhhhhhhhhhh.....hhhhhhhhhhh....eee..eee....eeee...hhhhhhhhhhhhhhhh.ee.....----.eeeeeeeee..eeeeeeeehhhheeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w8k A   7 DPLRPVVDASIQPLLKEHRIPGMAVAVLKDGKAHYFNYGVANRESGASVSEQTLFEIGsVSKTLTATLGAYAVVKGAMQLDDKASRHAPWLKGSVFDSITMGELATYSAGGLPLQFPEEVDSSEKMRAYYRQWAPVYSPGSHRQYSNPSIGLFGHLAASSLKQPFAQLMEQTLLPGLGMHHTYVNVPKQAMASYAYGYSKEDKPIRV--GMLADEAYGIKTSSADLLAFVKANIGGVDDKALQQAISLTHKGHYSVGGMTQGLGWESYAYPVTEQTLLAGNSAKVILEANPTAAPR----QVLFNKTGSSNGFGAYVAFVPARGIGIVMLANRNYPIPARVKAAHAILAQLAG 359
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      |216       226       236       246       256       266       276       286       296     |   -|      316       326       336       346       356   
                                                                                     65-SEP                                                                                                                                             213  |                                                                                   302  307                                                    
                                                                                                                                                                                                                                           216
   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  (0, 0)

(no "SCOP Domain" information available for 3W8K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W8K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W8K)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q51578_KLEPN | Q51578)
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.
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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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        Q51578_KLEPN | Q51578: 4wbg

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