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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE A FROM XANTHOMONAS ORYZAE PATHOVAR ORYZAE WITH ADP
 
Authors :  T. T. N. Doan, J. K. Kim, Y. J. Ahn, L. W. Kang
Date :  06 Apr 11  (Deposition) - 04 May 11  (Release) - 04 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Adp Forming Ligase, Dimerization Of Two D-Alanines, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. T. N. Doan, J. K. Kim, Y. J. Ahn, L. W. Kang
Crystal Structure Of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae With Adp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE 1
    Chains: A
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 342109
    Strain: MAFF 311018
    Synonym: D-ALANINE-D-ALANINE LIGASE A, D-ALA-D-ALA LIGASE 1, D- ALANYLALANINE SYNTHETASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:183 , LYS A:185 , SER A:192 , GLU A:221 , ALA A:222 , ALA A:223 , VAL A:224 , GLU A:228 , PHE A:304 , ASN A:314 , GLU A:315 , MG A:369 , HOH A:486 , HOH A:489 , HOH A:507BINDING SITE FOR RESIDUE ADP A 368
2AC2SOFTWAREASP A:302 , ASN A:314 , GLU A:315 , ADP A:368 , HOH A:447BINDING SITE FOR RESIDUE MG A 369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RFC)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:180 -Pro A:181
2Gly A:190 -Ser A:191
3Ile A:270 -Pro A:271
4Asp A:308 -Gly A:309

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RFC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RFC)

(-) Exons   (0, 0)

(no "Exon" information available for 3RFC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d3rfca1 A:2-139 automated matches                                                                                                       d3rfca2 A:140-364 automated matches                                                                                                                                                                              SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhhhh....eeeeeeee.....eeee.....ee........ee......eee........eee.........eeeeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh......eeeeehhhhh..hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhhhhh.eeeeee....eeeeeeeee....eeeeeeee...ee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfc A   2 RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVNDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQQALAQIDVVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADAFAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVEIVIPADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAV 364
                                    11        21        31        41        51        61        71        81        91|      103       113       123       133       143       153       163       173       183       193       203       213       223       233       243     ||270       280       290       300       310       320       330       340       350       360    
                                                                                                                    91|                                                                                                                                                        249|                                                                                                 
                                                                                                                     94                                                                                                                                                         267
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 Classification and Annotation

(-) SCOP Domains  (2, 2)

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 3RFC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RFC)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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3e5n CRYSTAL STRUCUTRE OF D-ALANINE-D-ALANINE LIGASE FROM XANTHOMONAS ORYZAE PV. ORYZAE KACC10331