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(-) Description

Title :  CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALANINE-D-ALANINE AND COPPER (II)
 
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 :  04 Jan 14  (Deposition) - 15 Jan 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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, 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
    Fragment: VANXYC
    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, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2CU2Ligand/IonCOPPER (II) ION
3DAL4Ligand/IonD-ALANINE
4MG1Ligand/IonMAGNESIUM ION
5PE34Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
6SO43Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:95 , ASP A:102 , HIS A:156 , DAL A:202BINDING SITE FOR RESIDUE CU A 201
02AC2SOFTWAREGLU A:142 , ASP A:143 , LYS A:144 , GLN A:145 , SER A:151 , TYR A:152 , HOH A:431BINDING SITE FOR RESIDUE SO4 A 204
03AC3SOFTWAREGLU A:66 , HOH A:326 , HOH A:352 , HOH A:415 , GLU B:66 , HOH B:420BINDING SITE FOR RESIDUE MG A 205
04AC4SOFTWAREASP B:112BINDING SITE FOR RESIDUE CL A 206
05AC5SOFTWAREARG A:69 , HOH B:393BINDING SITE FOR RESIDUE CL A 207
06AC6SOFTWARETHR A:63BINDING SITE FOR RESIDUE CL A 208
07AC7SOFTWAREHIS A:11 , HOH A:349BINDING SITE FOR RESIDUE CL A 209
08AC8SOFTWAREPHE A:189 , HOH A:465 , HIS B:179 , ALA B:183BINDING SITE FOR RESIDUE PE3 A 210
09AC9SOFTWAREHIS A:179 , ALA A:183 , HOH A:456 , PHE B:189BINDING SITE FOR RESIDUE PE3 A 211
10BC1SOFTWAREHIS B:95 , ASP B:102 , HIS B:156 , DAL B:202BINDING SITE FOR RESIDUE CU B 201
11BC2SOFTWAREPHE B:86 , HIS B:95 , ASP B:102 , ILE B:114 , TRP B:155 , HIS B:156 , CU B:201 , DAL B:203BINDING SITE FOR RESIDUE DAL B 202
12BC3SOFTWAREARG B:62 , GLN B:67 , PHE B:86 , ALA B:88 , SER B:93 , HIS B:95 , TYR B:140 , GLU B:153 , DAL B:202 , HOH B:301BINDING SITE FOR RESIDUE DAL B 203
13BC4SOFTWAREHIS A:21 , LEU A:22 , ARG B:68 , ARG B:69 , HOH B:328BINDING SITE FOR RESIDUE SO4 B 204
14BC5SOFTWARETHR A:63 , HOH A:352 , THR B:63 , LYS B:65 , ARG B:69 , HOH B:326BINDING SITE FOR RESIDUE SO4 B 205
15BC6SOFTWAREHIS B:11BINDING SITE FOR RESIDUE CL B 206
16BC7SOFTWAREASP B:143BINDING SITE FOR RESIDUE CL B 207
17BC8SOFTWAREMET B:1 , PRO B:20 , HIS B:21 , GLN B:35BINDING SITE FOR RESIDUE PE3 B 208
18BC9SOFTWARETRP B:173 , GLU B:177 , ASP B:180BINDING SITE FOR RESIDUE PE3 B 209
19CC1SOFTWAREGLN A:67 , PHE A:86 , ALA A:88 , SER A:93 , HIS A:95 , ASP A:102 , GLU A:153 , TRP A:155 , HIS A:156 , CU A:201 , HOH A:301BINDING SITE FOR LINKED RESIDUES A 202 to 203

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:115 -B:92

(-) 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 4OAK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OAK)

(-) 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:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee........eehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee...............hhhhhhhhhhhhhh.eeeee...hhhhhh...eeeeeee...hhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oak A   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQFA 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee........eehhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee...............hhhhhhhhhhhhhh.eeeee...hhhhhh...eeeeeee...hhhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oak B   1 MNTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQFA 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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 4OAK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4mus 4mut

(-) Related Entries Specified in the PDB File

4f78 CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG
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
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 RELATED ID: CSGID-IDP91778 RELATED DB: TARGETTRACK