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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
 
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 :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
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: 562
    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 Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric Unit (5, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DAL2Ligand/IonD-ALANINE
3PE31Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
4SO41Ligand/IonSULFATE ION
5ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAL2Ligand/IonD-ALANINE
3PE31Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2DAL1Ligand/IonD-ALANINE
3PE31Ligand/Ion3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
4SO4-1Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:95 , ASP A:102 , HIS A:156 , DAL A:202 , HOH A:468 , HOH A:469BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWAREGLN A:67 , PHE A:86 , ALA A:88 , SER A:93 , HIS A:95 , GLU A:153 , HIS A:156 , ZN A:201 , HOH A:406 , HOH A:407 , HOH A:408 , HOH A:468 , HOH A:469BINDING SITE FOR RESIDUE DAL A 202
3AC3SOFTWAREHIS A:21 , LEU A:22 , ARG B:69BINDING SITE FOR RESIDUE CL A 203
4AC4SOFTWAREASN A:2 , LEU A:6 , HIS A:179 , PHE B:189BINDING SITE FOR RESIDUE PE3 A 204
5AC5SOFTWAREHIS B:95 , ASP B:102 , HIS B:156 , DAL B:202 , HOH B:443 , HOH B:444BINDING SITE FOR RESIDUE ZN B 201
6AC6SOFTWAREARG B:62 , GLN B:67 , PHE B:86 , ALA B:88 , SER B:93 , HIS B:95 , TYR B:140 , GLU B:153 , ZN B:201 , HOH B:386 , HOH B:443 , HOH B:444 , HOH B:445BINDING SITE FOR RESIDUE DAL B 202
7AC7SOFTWAREARG A:119 , HOH A:335 , LYS B:65 , ARG B:68 , ARG B:69 , HOH B:366BINDING SITE FOR RESIDUE SO4 B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric 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 4MUT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MUT)

(-) Sequences/Alignments

Asymmetric 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:187
                                                                                                                                                                                                                           
               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...hhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mut A   2 NTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQ 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       


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...hhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mut B   2 NTLQLINKNHPLKKNQEPPHLVLAPFSDHDVYLQPEVAKQWERLVRATGLEKDIRLVSGYRTEKEQRRLWEYSLKENGLAYTKQFVALPGCSEHQIGLAIDVGLKKQEDDDLICPHFRDSAAADLFMQQMMNYGFILRYPEDKQEITGISYEPWHFRYVGLPHSQVITAQKWTLEEYHDYLAQTVRQF 189
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   Legend:   → Mismatch (orange background)
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  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 4MUT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

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 Related Entries

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        Q9JN36_ENTGA | Q9JN36: 4mur 4mus 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
4mus CRYSTAL STRUCTURE OF VANCOMYCIN RESISTANCE D,D-DIPEPTIDASE/ D,D-PENTAPEPTIDASE VANXYC D59S MUTANT IN COMPLEX WITH D-ALA -D-ALA PHOSPHINATE ANALOG
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)