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(-) Description

Title :  CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG
 
Authors :  P. J. Stogios, Z. Wawrzak, E. Evdokimova, G. Minasov, O. Egorova, R. Di M. Kudritska, V. Yim, D. Meziane-Cherif, P. Courvalin, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  15 May 12  (Deposition) - 23 May 12  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
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, Vancomycin Resistance, D-Alanine-D-Alanine, 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
    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: VANXYG, VANYG2
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Strain: BM4518
    Synonym: D,D-PEPTIDASE, VANXYG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 20)

Asymmetric/Biological Unit (6, 20)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3GOL3Ligand/IonGLYCEROL
4MSE4Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:107 , ASP A:114 , HIS A:167 , SO4 A:303 , HOH A:418BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREMSE A:2 , LYS A:3 , THR A:4 , LYS A:227BINDING SITE FOR RESIDUE CL A 302
03AC3SOFTWAREARG A:74 , GLN A:79 , VAL A:99 , ALA A:100 , SER A:105 , HIS A:107 , HIS A:167 , ZN A:301 , HOH A:424 , HOH A:460 , HOH A:483BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWARELYS A:120 , GLU A:157 , EDO A:310BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREPRO A:36 , ALA A:37 , ASN A:52 , GLN A:191 , HOH A:442 , HOH A:512 , HOH A:516BINDING SITE FOR RESIDUE EDO A 305
06AC6SOFTWAREGLU A:188 , PHE A:192 , HOH A:470BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREPRO A:218 , EDO A:308 , HOH A:431 , HOH A:491 , HOH A:524BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREASP A:199 , EDO A:307BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREASN A:21 , LYS A:22 , ILE A:158 , THR A:159BINDING SITE FOR RESIDUE EDO A 309
10BC1SOFTWARELYS A:97 , GLY A:160 , ILE A:161 , SER A:162 , EDO A:304BINDING SITE FOR RESIDUE EDO A 310
11BC2SOFTWAREGLY A:91 , GLU A:92 , ASP A:93 , HOH A:420BINDING SITE FOR RESIDUE EDO A 311
12BC3SOFTWAREGLU A:181 , PHE A:204 , GLU A:205 , HOH A:584BINDING SITE FOR RESIDUE EDO A 312
13BC4SOFTWAREASP A:144 , ARG A:209 , HOH A:531BINDING SITE FOR RESIDUE EDO A 313
14BC5SOFTWAREALA A:152 , ARG A:153 , ASP A:154BINDING SITE FOR RESIDUE GOL A 314
15BC6SOFTWAREASN A:65 , SER A:66 , LYS A:155BINDING SITE FOR RESIDUE GOL A 315
16BC7SOFTWARECYS A:14 , GLY A:15 , LEU A:18 , VAL A:31 , THR A:109 , HOH A:578 , HOH A:585BINDING SITE FOR RESIDUE GOL A 316

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F78)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:173 -Pro A:174
2His A:208 -Arg A:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F78)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F78)

(-) Exons   (0, 0)

(no "Exon" information available for 4F78)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhhh...................eee........eeehhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee..............hhhhhhhhhhhhhh.eee..hhhhhhhhh......eeee...hhhhhhhhhh.hhhhhhhhhh.......eeee.....eeeeeeee....eeeeeee...eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f78 A   0 GmmKTIELEKEEIYCGNLLLVNKNYPLRDNNVKGLVPADIRFPNILmKRDVANVLQLIFEKISAGNSIVPVSGYRSLEEQTAIYDGSLKDNGEDFTRKYVALPNHSEHQTGLAIDLGLNKKDIDFIRPDFPYDGICDEFRRAAPDYGFTQRYARDKEEITGISHEPWHFRYVGYPHSKImQENGFSLEEYTQFIKAYLEDNKYLFEQAHRAEIEIYYVPAKDDKTLIKIPENCVYQISGNNIDGFVVTIWR 250
                             ||      9        19        29        39      | 49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
                             ||                                          46-MSE                                                                                                                              179-MSE                                                                   
                             1-MSE                                                                                                                                                                                                                                                     
                              2-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4F78)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F78)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F78)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    His A:208 - Arg A:209   [ RasMol ]  
    Tyr A:173 - Pro A:174   [ RasMol ]  
 

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  4f78
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 Related Entries

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        Q9KHL8_ENTFL | Q9KHL8: 4muq

(-) Related Entries Specified in the PDB File

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
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)