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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM ACINETOBACTER BAUMANNII
 
Authors :  K. H. Huynh, M. K. Hong, L. W. Kang
Date :  17 Aug 15  (Deposition) - 17 Aug 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  D,F  (1x)
Keywords :  D-Alanine-D-Alanine Ligase, Acinetobacter Baumannii, Apo Structure, Drug Target, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. H. Huynh, M. K. Hong, C. Lee, H. T. Tran, S. H. Lee, Y. J. Ahn, S. S. Cha, L. W. Kang
The Crystal Structure Of The D-Alanine-D-Alanine Ligase Fro Acinetobacter Baumannii Suggests A Flexible Conformational Change In The Central Domain Before Nucleotide Binding
J. Microbiol. V. 53 776 2015
PubMed-ID: 26502962  |  Reference-DOI: 10.1007/S12275-015-5475-8

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A, B, C, D, E, F
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DDL, ACICU_03532
    Organism Scientific: ACINETOBACTER BAUMANNII ACICU
    Organism Taxid: 405416
    Strain: ACICU
    Synonym: D-ALA-D-ALA LIGASE,D-ALANYLALANINE SYNTHETASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C   
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):    D F

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5D8D)

(-) Sites  (0, 0)

(no "Site" information available for 5D8D)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D8D)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Leu A:135 -Pro A:136
2Ile A:223 -Pro A:224
3Leu B:135 -Pro B:136
4Ile B:223 -Pro B:224
5Leu C:135 -Pro C:136
6Ile C:223 -Pro C:224
7Leu D:135 -Pro D:136
8Ile D:223 -Pro D:224
9Leu E:135 -Pro E:136
10Ile E:223 -Pro E:224
11Ile F:223 -Pro F:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D8D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D8D)

(-) Exons   (0, 0)

(no "Exon" information available for 5D8D)

(-) 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:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeeee........eee....hhhhhhhhhhhhh..eeeee...eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d8d A   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHEGSVGMSKVEKAEDFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTL 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   ||  152       162       172       182       192       222       232       242       252       262       272       282       292       302  
                                                                                                                                                                         145|                                                  200|                                                                                   
                                                                                                                                                                          147                                                   221                                                                                   


Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeeee........eee.hhhhhhhhhhhhhh....eeeee...eeeeeeeee..ee...eee........hhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d8d B   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHESSVGMSKVEKAEDFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTL 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  ||   152       162       172       182       192       222       232       242       252       262       272       282       292       302  
                                                                                                                                                                        144|                                                   200|                                                                                   
                                                                                                                                                                         146                                                    221                                                                                   


Chain C from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eee.....hhhhhhhhhh..eeeee..........hhhhhhhhhh..eeeee...eeeeeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8d C   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHEVGMSKFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTL 304
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  ||   160       170       180       190       200|      230       240       250       260       270       280       290       300    
                                                                                                                                                                        144| 152|                                      200|                                                                                   
                                                                                                                                                                         148  159                                       221                                                                                   


Chain D from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.eeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhh..eeeee.........eee...hhhhhhhhhhhh....eeeee...eeeeeeeee..ee...eee........hhhhhhhhhhhhhhhhhhh....eeeeeeeee....eeeeeee........hhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8d D   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHEGSSVGMSKVEKAEDFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       221       231       241       251       261       271       281       291       301    
                                                                                                                                                                                                                                200|                                                                                    
                                                                                                                                                                                                                                 221                                                                                    


Chain E from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhh..eeeee.....eee..hhhhhh......eeeee....eeeeeeee..ee...ee........hhhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5d8d E   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIITKETDLDSVIAELGLPVIIKPVHVGMSKVAEDFAAAIEKATAVVMAEKWITGREFTISFLNGQPLPVIRLQGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLEGT 307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 ||    157       167|      180       190       200|      231       241       251       261       271       281       291       301      
                                                                                                                                                                       143|  153|        167|                          200|                                                                                     
                                                                                                                                                                        148   156         171                           222                                                                                     


Chain F from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhheeeee......hhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhh.eeee.........hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh.......eee...hhhhhhhhh...................hhhhh.hhhhhh.....eee.......eeeeee..ee...ee.........hhhhhhhhhhhhhhhhhhh.....eeeeeeee...eeeeeeee........hhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d8d F   2 SNATKFGKVAVLLGGKSAERAVSLDSGQAVLDALLRSGVQAEAFDPQDRSVTELVNYDRAFIVLHGRGGEDGQIQGVLEWLNIPYTGTGVQGSAIGMDKVKTKQIWQGSDLPTAPYRIIETDLDSVIAELIIKPVHEGSSVGMSKVEKAEDFAAAIEKATQHDAVVMAEKWITGREFTISFLNGQPLPVIRLQYGIPCGLSETEEKKLQALCLRAFQAVGAEGWGRIDAMQDEQGNFWLLEVNTVPGMTSHSLVPKAAKAVGYSFDELCVAILEQTLE 305
                                    11        21        31        41        51        61        71        81        91       101       111       123       133|      147       157       167       177       187       197  ||   227       237       247       257       267       277       287       297        
                                                                                                                                                120|       133|                                                           200|                                                                                    
                                                                                                                                                 123        138                                                            221
   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  (0, 0)

(no "SCOP Domain" information available for 5D8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D8D)

(-) Gene Ontology  (12, 12)

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  Cis Peptide Bonds
    Ile A:223 - Pro A:224   [ RasMol ]  
    Ile B:223 - Pro B:224   [ RasMol ]  
    Ile C:223 - Pro C:224   [ RasMol ]  
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