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(-) Description

Title :  CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D-PENTAPEPTIDASE VANXYC D59S MUTANT
 
Authors :  P. J. Stogios, E. Evdokimova, D. Meziane-Cherif, R. Di Leo, V. Yim, P. C A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
Date :  23 Sep 13  (Deposition) - 02 Oct 13  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Center For Structural Genomics Of Infectious Diseases, Csgid, National Institute Of Allergy And Infectious Diseases, Niaid, Alpha+Beta Protein, Metallopeptidase, Hedgehog/Dd-Peptidase Fold, Merops M15B Subfamily, Zn2+-Dependent D, D-Dipeptidase, Zn2+- Dependent D, D-Pentapeptidase, Vancomycin Resistance, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Meziane-Cherif, P. J. Stogios, E. Evdokimova, A. Savchenko, P. Courvalin
Structural Basis For The Evolution Of Vancomycin Resistance D, D-Peptidases.
Proc. Natl. Acad. Sci. Usa V. 111 5872 2014
PubMed-ID: 24711382  |  Reference-DOI: 10.1073/PNAS.1402259111

(-) Compounds

Molecule 1 - D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VANXYC
    Mutation: YES
    Organism Scientific: ENTEROCOCCUS GALLINARUM
    Organism Taxid: 1353
    Strain: BM4174
    Synonym: D,D-DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYC

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2PE34Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
3SO41Ligand/IonSULFATE ION
4ZN2Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , ASP A:102 , HIS A:156 , HOH A:383 , HOH A:465BINDING SITE FOR RESIDUE ZN A 201
02AC2SOFTWAREGLN A:67 , ALA A:88 , SER A:93 , HOH A:598BINDING SITE FOR RESIDUE CL A 202
03AC3SOFTWAREARG A:69 , HOH A:528 , LEU B:22BINDING SITE FOR RESIDUE CL A 203
04AC4SOFTWAREASN A:8 , ASN A:10 , HIS A:11 , HOH A:470BINDING SITE FOR RESIDUE CL A 204
05AC5SOFTWAREHIS A:179BINDING SITE FOR RESIDUE PE3 A 205
06AC6SOFTWAREMET A:1 , ASN A:2 , GLN A:5 , LYS A:14 , GLN A:17BINDING SITE FOR RESIDUE PE3 A 206
07AC7SOFTWAREGLU A:37 , LYS A:40 , GLN A:41 , ARG A:44BINDING SITE FOR RESIDUE PE3 A 207
08AC8SOFTWAREPHE A:189 , HIS B:179 , ALA B:183 , HOH B:574BINDING SITE FOR RESIDUE PE3 A 208
09AC9SOFTWAREHIS B:95 , ASP B:102 , HIS B:156 , HOH B:353 , HOH B:385BINDING SITE FOR RESIDUE ZN B 201
10BC1SOFTWAREARG A:119 , LYS B:65 , ARG B:68 , ARG B:69 , HOH B:411 , HOH B:480 , HOH B:563BINDING SITE FOR RESIDUE SO4 B 202
11BC2SOFTWAREGLN B:67 , ALA B:88 , HOH B:583BINDING SITE FOR RESIDUE CL B 203
12BC3SOFTWAREHIS A:21 , LEU A:22 , HOH A:580 , ARG B:69BINDING SITE FOR RESIDUE CL B 204
13BC4SOFTWAREHOH A:538 , THR B:63 , HOH B:436BINDING SITE FOR RESIDUE CL B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MUR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:162 -Pro A:163
2Leu B:162 -Pro B:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MUR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MUR)

(-) Exons   (0, 0)

(no "Exon" information available for 4MUR)

(-) 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:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee........eehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee...............hhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mur A   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQF 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180         


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee........eehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee...............hhhhhhhhhhhhhh.eee.....hhhhhh......eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mur B   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQF 189
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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 4MUR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MUR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MUR)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9JN36_ENTGA | Q9JN36: 4mus 4mut 4oak

(-) Related Entries Specified in the PDB File

4f78 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE BIFUNCTIONAL D,D -DIPEPTIDASE/D,D-CARBOXYPEPTIDASE VANXYG FROM ENTEROCOCCUS FAECALIS
4muq CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG IN COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG
4mus CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA -D-ALA PHOSPHINATE ANALOG
4mut CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D- ALANINE
4oak CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D- ALANINE-D-ALANINE AND COPPER (II)