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(-) Description

Title :  CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE VANXYG 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 :  1.36
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, 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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15-TC LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VANXYG
    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, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
12D81Ligand/Ion(2R)-3-[(R)-[(1S)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4LY01Ligand/Ion(2R)-3-[(R)-[(1R)-1-AMINOETHYL](HYDROXY)PHOSPHORYL]-2-METHYLPROPANOIC ACID
5PE34Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
6ZN1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:107 , ASP A:114 , HIS A:167 , LY0 A:302 , 2D8 A:303BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREARG A:74 , GLN A:79 , TYR A:98 , ALA A:100 , SER A:105 , HIS A:107 , ASP A:114 , ILE A:125 , GLU A:164 , TRP A:166 , HIS A:167 , ZN A:301 , HOH A:419BINDING SITE FOR RESIDUE LY0 A 302
03AC3SOFTWAREARG A:74 , GLN A:79 , TYR A:98 , ALA A:100 , SER A:105 , HIS A:107 , ASP A:114 , ILE A:125 , GLU A:164 , TRP A:166 , HIS A:167 , ZN A:301 , HOH A:419BINDING SITE FOR RESIDUE 2D8 A 303
04AC4SOFTWARELYS A:97 , GLU A:156 , ILE A:161 , SER A:162 , HOH A:587 , HOH A:671BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWAREARG A:153 , ASP A:154 , HOH A:627 , HOH A:656BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREASN A:65 , SER A:66 , HOH A:606BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREASN A:21 , LYS A:22 , ASN A:23 , ARG A:40 , GLU A:157 , ILE A:158 , THR A:159 , HOH A:502BINDING SITE FOR RESIDUE PE3 A 307
08AC8SOFTWAREVAL A:233 , TYR A:234 , GLN A:235BINDING SITE FOR RESIDUE PE3 A 308
09AC9SOFTWARELEU A:87 , LYS A:88 , ASN A:90 , GLY A:91 , GLU A:92 , ASP A:93 , HOH A:452BINDING SITE FOR RESIDUE PE3 A 309
10BC1SOFTWARELYS A:32 , GLY A:33 , ARG A:48BINDING SITE FOR RESIDUE PE3 A 310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:173 -Pro A:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUQ)

(-) 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...................eeeee..eeeeeeehhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eeeeee..............hhhhhhhhhhhhhh.eee..hhhhhhhhh......eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhheee.......eeeeeee....eeeeeee...eeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4muq 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
   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 4MUQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
        Q9KHL8_ENTFL | Q9KHL8: 4f78

(-) Related Entries Specified in the PDB File

4f78 APO CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D- DIPEPTIDASE VANXYG RELATED ID: IDP91774 RELATED DB: TARGETTRACK
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)