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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM BURKHOLDERIA XENOVORANS
 
Authors :  Ssgcid, Seattle Structural Genomics Center For Infectious Dis (Ssgcid)
Date :  31 Mar 12  (Deposition) - 18 Jul 12  (Release) - 30 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A (1x),C (1x)
Biol. Unit 6:  B (1x),D (1x)
Keywords :  Ssgcid, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, D-Alanine-D-Alanine Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, L. A. Gallagher, R. Patrapuvich, M. C. Clifton, A. S. Gardberg, T. E. Edwards, B. Armour, D. W. Begley, S. H. Dieterich, D. M. Dranow, J. Abendroth, J. W. Fairman, D. Fox, B. L. Staker, I. Phan, A. Gillespie, R. Choi, S. Nakazawa-Hewitt, M. T. Nguyen, A. Napuli, L. Barrett, G. W. Buchko, R. Stacy, P. J. Myler, L. J. Stewart, C. Manoil W. C. Van Voorhis
Combining Functional And Structural Genomics To Sample The Essential Burkholderia Structome.
Plos One V. 8 53851 2013
PubMed-ID: 23382856  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053851

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B, C, D
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BXENO_A3907, BXE_A0488, DDL
    Organism Scientific: BURKHOLDERIA XENOVORANS
    Organism Taxid: 266265
    Strain: LB400
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): A (1x) C (1x) 
Biological Unit 6 (1x):  B (1x) D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4EGJ)

(-) Sites  (0, 0)

(no "Site" information available for 4EGJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Leu A:143 -Pro A:144
2Ile A:230 -Pro A:231
3Leu B:143 -Pro B:144
4Ile B:230 -Pro B:231
5Leu C:143 -Pro C:144
6Ile C:230 -Pro C:231
7Leu D:143 -Pro D:144
8Ile D:230 -Pro D:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EGJ)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4egja1 A:4-102 automated matches                                                                  d4egja2 A:103-311 automated matches                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee...ee.hhhhhhhhhhhhh....eeeeee...eeeeeeeeee.......eee...ee.....hhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egj A   4 IDPKQFGKVAVLLGGNSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQLGIPTPPFEAVLRGDDYEARAKEIVAKLGLPLFVKPASIKVKSADALPAALIEAVKFDRIVVVEKSIEGGGEYTACIAGNLDLPVIRIVPQYLIPCGLTADEEARLKVLARRAFDVLGCTDWGRADFMLDADGNPYFLEVNTAPGMTDHSLPPKAARAVGISYQELVVAVLALTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       160       170       180       190       200       210|      236       246       256       266       276       286       296       306     
                                                                                                                                                                             151|                                                210|                                                                                    
                                                                                                                                                                              159                                                 227                                                                                    


Chain B from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4egjb1 B:4-102 automated matches                                                                  d4egjb2 B:103-311 automated matches                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee....ee.hhhhhhhhhhhhh....eeeeee...eeeeeeeeee.......eee.........hhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egj B   4 IDPKQFGKVAVLLGGNSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQLGIPTPPFEAVLRGDDYEARAKEIVAKLGLPLFVKPASEIKVKSADALPAALIEAVKFDRIVVVEKSIEGGGEYTACIAGNLDLPVIRIVQYLIPCGLTADEEARLKVLARRAFDVLGCTDWGRADFMLDADGNPYFLEVNTAPGMTDHSLPPKAARAVGISYQELVVAVLALTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       159       169       179       189       199       209|      236       246       256       266       276       286       296       306     
                                                                                                                                                                              152|                                               209|                                                                                    
                                                                                                                                                                               159                                                227                                                                                    


Chain C from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4egjc1 C:4-102 automated matches                                                                  d4egjc2 C:103-312 automated matches                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhh....eeee.ee.hhhhhhhhhhhhh....eeeeee...eeeeeeeeee.......eeee.......eee.....hhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egj C   4 IDPKQFGKVAVLLGGNSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQLGIPTPPFEAVLRGDDYEARALGLPLFVKIKVKSADALPAALIEAVKFDRIVVVEKSIEGGGEYTACIAGNLDLPVIRIVPAGENDTQYLIPCGLTADEEARLKVLARRAFDVLGCTDWGRADFMLDADGNPYFLEVNTAPGMTDHSLPPKAARAVGISYQELVVAVLALTLK 312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133||     159       169       179       189       199       209   ||  229       239       249       259       269       279       289       299       309   
                                                                                                                                                            134|    148|                                                   213|                                                                                        
                                                                                                                                                             141     159                                                    224                                                                                        


Chain D from PDB  Type:PROTEIN  Length:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4egjd1 D:3-102 automated matches                                                                   d4egjd2 D:103-312 automated matches                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeee...hhhhh.hhhhhhhhhhh.ee...hhhhhhhhhhhhhhhhhhhhh......ee....eee...eee...eeeeeeeeee.......eeee...eee.....hhhhhhhhhhhhhhhhhh.....eeeeeeeee....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4egj D   3 SIDPKQFGKVAVLLGGNSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAERPLAALKEEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQLGIPTPPFEAGLPLFVKVVVEKSIEGGGEYTACIAGNLDLPVIRIVPATQYLIPCGLTADEEARLKVLARRAFDVLGCTDWGRADFMLDADGNPYFLEVNTAPGMTDHSLPPKAARAVGISYQELVVAVLALTLK 312
                                    12        22        32        42        52        62        72        82        92       102       112       122||     182       192       202       226       236       246       256       266       276       286       296       306      
                                                                                                                                                  123|   148|                           211|                                                                                      
                                                                                                                                                   142    181                            226
   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, 8)

Asymmetric 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 4EGJ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:230 - Pro A:231   [ RasMol ]  
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