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(-) Description

Title :  CRYSTAL STRUCTURE OF VANG D-ALA:D-SER LIGASE FROM ENTEROCOCCUS FAECALIS
 
Authors :  D. Meziane-Cherif, F. A. Saul, A. Haouz, P. Courvalin
Date :  28 Jun 12  (Deposition) - 19 Sep 12  (Release) - 13 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Vancomycin Resistance, Peptidoglycan Synthesis, D-Ala:D-Ser Ligase, Atp-Grasp Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Meziane-Cherif, F. A. Saul, A. Haouz, P. Courvalin
Structural And Functional Characterization Of Vang D-Ala:D-Ser Ligase Associated With Vancomycin Resistance In Enterococcus Faecalis
J. Biol. Chem. V. 287 37583 2012
PubMed-ID: 22969085  |  Reference-DOI: 10.1074/JBC.M112.405522

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE 7
    Chains: A, B
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PAT911 [PET28A(+) VANG]
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDL7, VANG
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Strain: BM4518
    Synonym: D-ALA-D-ALA LIGASE 7, D-ALANYLALANINE SYNTHETASE 7

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2SO49Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:140 , PHE A:181 , LYS A:183 , SER A:190 , ILE A:193 , GLU A:219 , GLU A:220 , THR A:221 , ILE A:222 , GLU A:226 , LEU A:247 , TYR A:258 , LYS A:261 , PHE A:301 , ASN A:311 , GLU A:312 , HOH A:556 , HOH A:588 , HOH A:593 , HOH A:637 , TYR B:258BINDING SITE FOR RESIDUE ADP A 401
02AC2SOFTWAREARG A:297 , ASN A:314 , PRO A:317 , GLY A:318 , HOH A:501 , HOH A:525 , HOH A:575 , LYS B:257BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREASN A:223 , THR A:303 , PRO A:304 , SER A:305BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWARESER A:335 , PHE A:336 , HOH A:611 , HOH A:612BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWARELYS A:108 , GLY A:188 , SER A:189 , HOH A:640BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREPHE B:181 , LYS B:183 , SER B:190 , ILE B:193 , GLU B:219 , GLU B:220 , THR B:221 , ILE B:222 , GLU B:226 , LEU B:247 , PHE B:252 , PHE B:301 , ASN B:311 , GLU B:312 , HOH B:503 , HOH B:529 , HOH B:540 , HOH B:617 , HOH B:649BINDING SITE FOR RESIDUE ADP B 401
07AC7SOFTWAREARG B:297 , GLY B:318 , SER B:323 , ARG B:324 , HOH B:501 , HOH B:514 , HOH B:633 , HOH B:641BINDING SITE FOR RESIDUE SO4 B 402
08AC8SOFTWAREASN B:223 , THR B:303 , PRO B:304 , SER B:305 , HOH B:594 , HOH B:600BINDING SITE FOR RESIDUE SO4 B 403
09AC9SOFTWARETYR A:254 , ALA B:187 , GLY B:188 , SER B:189 , HIS B:212BINDING SITE FOR RESIDUE SO4 B 404
10BC1SOFTWARELYS A:330 , LYS B:264 , TYR B:266 , ARG B:270BINDING SITE FOR RESIDUE SO4 B 405
11BC2SOFTWARELYS B:330 , SER B:335 , PHE B:336BINDING SITE FOR RESIDUE SO4 B 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FU0)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:178 -Pro A:179
2Met A:267 -Pro A:268
3Tyr B:178 -Pro B:179
4Met B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FU0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FU0)

(-) Exons   (0, 0)

(no "Exon" information available for 4FU0)

(-) 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:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fu0a1 A:2-138 automated matches                                                                                                    d4fu0a2 A:139-348 automated matches                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee...hhhhhh.hhhhhhh.eeeeee.......eeee..eeee..eeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeeee...eee...eeeeehhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fu0 A   2 QNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYV 348
                                    11        21        31        41        51        61        71        81      ||95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   
                                                                                                                 88|                                                                                                                                                                                                                                                               
                                                                                                                  93                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:343
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4fu0b1 B:2-138 automated matches                                                                                                    d4fu0b2 B:139-348 automated matches                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee...hhhhhh.....hhh.eeeeee.......eeee..eeee..eeee...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhh...eeeee.........eee.hhhhhhhhhhhhhh...eeeeee....eeeeeeeee....ee...eeeee...............eeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fu0 B   2 QNKKIAVIFGGNSTEYEVSLQSASAVFENINTNKFDIIPIGITRSGEWYHYTGEKEKILNNTWFEDSKNLCPVVVSQNRSVKGFLEIYRIIKVDLVFPVLHGKNGEDGTLQGIFELAGIPVVGCDTLSSALCMDKDRAHKLVSLAGISVPKSVTFKRFNEEAAMKEIEANLTYPLFIKPVRAGSSFGITKVIEKQELDAAIELAFEHDTEVIVEETINGFEVGCAVLGIDELIVGRVDEIELSSGFFDYTEKYTLKSSKIYMPARIDAEAEKRIQEAAVTIYKALGCSGFSRVDMFYTPSGEIVFNEVNTIPGFTSHSRYPNMMKGIGLSFSQMLDKLIGLYV 348
                                    11        21        31        41        51        61        71        81      ||95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   
                                                                                                                 88|                                                                                                                                                                                                                                                               
                                                                                                                  93
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FU0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FU0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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