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(-) Description

Title :  CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA-D-ALA PHOSPHINATE ANALOG
 
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) - 09 Oct 13  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
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, Antibiotic Resistance, Vancomycin 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  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
12D82Ligand/Ion(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4LY02Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
5SO41Ligand/IonSULFATE ION
6ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , ASP A:102 , HIS A:156 , 2D8 A:202 , LY0 A:203BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREARG A:62 , GLN A:67 , LEU A:70 , PHE A:86 , ALA A:88 , SER A:93 , HIS A:95 , ASP A:102 , ILE A:114 , GLU A:153 , TRP A:155 , HIS A:156 , ZN A:201 , HOH A:333 , HOH A:446BINDING SITE FOR RESIDUE 2D8 A 202
3AC3SOFTWAREARG A:62 , GLN A:67 , PHE A:86 , ALA A:88 , SER A:93 , HIS A:95 , ASP A:102 , ILE A:114 , GLU A:153 , TRP A:155 , HIS A:156 , ZN A:201 , HOH A:333BINDING SITE FOR RESIDUE LY0 A 203
4AC4SOFTWARELYS A:65 , ARG A:68 , ARG A:69 , HOH A:499 , HOH A:506 , ARG B:119BINDING SITE FOR RESIDUE SO4 A 204
5AC5SOFTWARELEU A:6 , ASN A:8 , ASN A:10 , HIS A:11 , LYS A:53 , GLU A:176 , ASP A:180 , HOH A:440 , HOH A:449 , HOH A:520BINDING SITE FOR RESIDUE GOL A 205
6AC6SOFTWAREHIS B:95 , ASP B:102 , HIS B:156 , LY0 B:202 , 2D8 B:203BINDING SITE FOR RESIDUE ZN B 201
7AC7SOFTWAREARG A:69 , HIS B:21 , LEU B:22BINDING SITE FOR RESIDUE CL A 206
8AC8SOFTWAREARG B:62 , GLN B:67 , PHE B:86 , ALA B:88 , SER B:93 , HIS B:95 , ASP B:102 , ILE B:114 , TYR B:140 , GLU B:153 , TRP B:155 , HIS B:156 , ZN B:201 , HOH B:358BINDING SITE FOR RESIDUE LY0 B 202
9AC9SOFTWAREARG B:62 , GLN B:67 , PHE B:86 , ALA B:88 , SER B:93 , HIS B:95 , ASP B:102 , LEU B:113 , ILE B:114 , TYR B:140 , GLU B:153 , TRP B:155 , HIS B:156 , ZN B:201 , HOH B:358BINDING SITE FOR RESIDUE 2D8 B 203

(-) SS Bonds  (0, 0)

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

(-) 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 4MUS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUS)

(-) 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:188
                                                                                                                                                                                                                            
               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.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mus A   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQ 188
                                    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:188
                                                                                                                                                                                                                            
               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..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mus B   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQ 188
                                    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 4MUS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        Q9JN36_ENTGA | Q9JN36: 4mur 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
4mur CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ D,D-PENTAPEPTIDASE VANXYC D59S MUTANT
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)