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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, B. M. Lee, L. W. Kang
Date :  25 Aug 13  (Deposition) - 19 Feb 14  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Adp-Depending Enzyme, D-Alanine-D-Alanine Ligase, Nucleotide Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. N. Doan, J. K. Kim, H. P. T. Ngo, H. T. Tran, S. S. Cha, K. M. Chung, K. H. Huynh, Y. J. Ahn, L. W. Kang
Crystal Structures Of D-Alanine-D-Alanine Ligase From Xanthomonas Oryzae Pv. Oryzae Alone And In Complex With Nucleotides
Arch. Biochem. Biophys. V. 545C 92 2014
PubMed-ID: 24440607  |  Reference-DOI: 10.1016/J.ABB.2014.01.009

(-) Compounds

Molecule 1 - D-ALANINE--D-ALANINE LIGASE
    Chains: A
    EC Number: 6.3.2.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDLA, DDL, XOO0352
    Mutation: YES
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 291331
    Strain: KACC10331
    Synonym: D-ALA-D-ALA LIGASE, D-ALANYLALANINE SYNTHETASE

 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
1AC1SOFTWAREASP A:302 , ASN A:314 , GLU A:315 , ADP A:402 , HOH A:552 , HOH A:666BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREPHE A:183 , LYS A:185 , GLU A:221 , ALA A:222 , ALA A:223 , VAL A:224 , GLU A:228 , PHE A:304 , GLU A:315 , MG A:401 , HOH A:575 , HOH A:666BINDING SITE FOR RESIDUE ADP A 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ME6)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:180 -Pro A:181
2Ile A:270 -Pro A:271

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ME6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ME6)

(-) Exons   (0, 0)

(no "Exon" information available for 4ME6)

(-) Sequences/Alignments

Asymmetric Unit
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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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4me6a1 A:2-139 automated matches                                                                                                    d4me6a2 A:140-365 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..ee..eeeee......hhhhhhhhhh..eeeee......eee.hhhhhhhhhhhhhh...eeeeee....eeeeeeeee....eeeeeeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4me6 A   2 RKIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVNDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQAQIDVVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAHADVDTLIAQLGLPLFVKPANQVGVSQVRTADAFAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVEIVIPADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAVE 365
                                    11        21        31        41        51        61        71        81        91|      106       116       126       136       146       156       166|      177       187 ||    200       210       220       230       240       268       278       288       298       308       318       328       338       348       358       
                                                                                                                    91|                                                                  166|                  189|                                                    248|                                                                                                  
                                                                                                                     97                                                                   168                   193                                                     267
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 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 4ME6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ME6)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q5H614_XANOR | Q5H614: 3r5f 4l1k

(-) Related Entries Specified in the PDB File

3e5n THE APO ENZYME- D-ALANINE-D-ALANINE LIGASE
3r5f THE SAME PROTEIN COMPLEXED WITH ATP
4l1k THE SAME PROTEIN COMPLEXED WITH AMPPNP