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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE B FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  31 Mar 12  (Deposition) - 11 Apr 12  (Release) - 11 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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),B (1x),C (1x),D (1x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Flexible Protein, Atp-Dependent, Magnesium Dependent, Cell Wall Biogenesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, J. W. Fairman, J. Abendroth, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of D-Alanine-D-Alanine Ligase B From Burkholderia Pseudomallei
To Be Published
PubMed: search

(-) 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 Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: BURPS1710B_3542, DDL
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B
    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)B (1x)C (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4EGQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EGQ)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4egqa1 A:4-102 automated matches                                                                  d4egqa2 A:103-311 automated matches                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeeee......eee.hhhhhhhhhhhhhhhh.eeeeee......eeeeeee.......eee.........hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4egq A   4 IDPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGIPTPPFETVMRGDDYAARAQDIVAKLGVPLFVKPASSVAVEKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADLDLPLIRIVPYLIPCGLDAAKEAEFKRIARRAFDVLGCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELVVKVLSLTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       156       166       176       186       196       206   ||  233       243       253       263       273       283       293       303        
                                                                                                                                                                             151|                                                    210|                                                                                   
                                                                                                                                                                              155                                                     228                                                                                   


Chain B from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4egqb1 B:5-102 automated matches                                                                 d4egqb2 B:103-312 automated matches                                                                                                                                                                          SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhh..eeeee...eee.hhhhhhhhhhhhhhhh.eeeeee......eeeeeee.......eeee.................eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egq B   5 DPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGIPTPPFETVMRGDDYAARAQDIVAKLGVPLFVKPASVEKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADLDLPLIRIVPAGEFYDYHAKYIANDTQYLIPCGLDAAKEAEFKRIARRAFDVLGCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELVVKVLSLTLD 312
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144      |160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
                                                                                                                                                                            151|                                                                                                                                                          
                                                                                                                                                                             158                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4egqc1 C:4-102 automated matches                                                                  d4egqc2 C:103-311 automated matches                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeeee...eee.hhhhhhhhhhhhhhhhheeeeee......eeeeeee.......eeeehhhhh.hhhhhhh....eee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4egq C   4 IDPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGIPTPPFETVMRGDDYAARAQDIVAKLGVPLFVKPAAVEKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADLDLPLIRIVPAGEFYDYHAKYIANDTQYLIPCGLDAAKEAEFKRIARRAFDVLGCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELVVKVLSLTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143      |159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309  
                                                                                                                                                                            150|                                                                                                                                                          
                                                                                                                                                                             157                                                                                                                                                          


Chain D from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4egqd1 D:4-102 automated matches                                                                  d4egqd2 D:103-311 automated matches                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh...eeee...hhhhh.hhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeeee......eeeeeee.......eee.....ee.....ee...ee.....hhhhhhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........hhhhhhhhhh..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4egq D   4 IDPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQRPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALGLDKFRTKLVWQQTGIPTPPFETVMRDYAARAQDIVAKLGVPLFVKPALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADLDLPLIRIVPAGEFYDYHAKYIANQYLIPCGLDAAKEAEFKRIARRAFDVLGCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSELVVKVLSLTL 311
                                    13        23        33        43        53        63        73        83        93       103       113       123  ||   135       145   ||  171       181       191       201       211       221  ||   233       243       253       263       273       283       293       303        
                                                                                                                                                    126|                 149|                                                       224|                                                                                    
                                                                                                                                                     129                  166                                                        227
   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  (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 4EGQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ile A:230 - Pro A:231   [ RasMol ]  
    Ile B:230 - Pro B:231   [ RasMol ]  
    Ile C:230 - Pro C:231   [ RasMol ]  
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(-) Related Entries Specified in the PDB File

4eg0 SAME PROTEIN BURKHOLDERIA AMBIFARIA, BUAMA.00119.A RELATED ID: BUPSA.00119.A RELATED DB: TARGETTRACK
4egj CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM BURKHOLDERIA XENOVORANS