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(-) Description

Title :  CRYSTAL STRUCTURE OF D-ALANINE-D-ALNINE LIGASE FROM XANTHOMONAS ORYZAE PV. ORYZAE WITH ATP
 
Authors :  T. T. N. Doan, J. K. Kim, L. W. Kang
Date :  18 Mar 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Xoddl-Atp Complex, Atp-Grasp Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. T. N. Doan, J. K. Kim, L. W. Kang
Crystal Structure Of D-Alanine-D-Alanine Ligase A From Xanthomonas Oryzae Pathovar Oryzae With Atp
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: HIS-TEV-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: 291331
    Strain: KACC10331
    Synonym: 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
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:141 , PHE A:183 , LYS A:185 , SER A:191 , 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:476 , HOH A:479BINDING SITE FOR RESIDUE ATP A 368
2AC2SOFTWAREASP A:302 , ASN A:314 , GLU A:315 , ATP A:368 , HOH A:480BINDING SITE FOR RESIDUE MG A 369

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3R5F)

(-) 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 3R5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3R5F)

(-) Exons   (0, 0)

(no "Exon" information available for 3R5F)

(-) 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:343
 aligned with Q5H614_XANOR | Q5H614 from UniProtKB/TrEMBL  Length:347

    Alignment length:363
                                              1                                                                                                                                                                                                                                                                                                                                                        
                                     -        |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342   
         Q5H614_XANOR     - ------------------MQSARNILDALDPQRFEPVLIGIDKQGQWHVNDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQPEQALAQIDVVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADAFAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVVHDAFYSYATKYISEHGAEIVIPADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGFTRISMYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAVE 345
               SCOP domains d3r5fa1 A:3-139 automated matches                                                                                                        d3r5fa2 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..eeeeehhhhh..hhhhhhhhhh..eeeee.........eee.hhhhhhhhhhhhh....eeeeee....eeeeeeee.....eeeeeeee..-----------------.ee.....hhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r5f A   3 KIRVGLIFGGKSAEHEVSLQSARNILDALDPQRFEPVLIGIDKQGQWHVNDPDSFLLHADDPARIALHRSGRGVALLPGAQQQQLRPIQ---ALAQIDVVFPIVHGTLGEDGSLQGLLRMANLPFVGSGVLGSAVAMDKDMAKRVLRDARLAVAPFVCFDRHTAAHADVDTLIAQLGLPLFVKPANQGSSVGVSQVRTADAFAAALALALAYDHKVLVEAAVAGREIECAVLGNAVPHASVCGEVVV-----------------EIVIPADIDAQTQQRIQQIAVQAYQALGCAGMARVDVFLCADGRIVINEVNTLPGFTRISVYPKLWQASGLDYRGLITRLIELALERHTDDQLLRSAVE 365
                                    12        22        32        42        52        62        72        82        |-  |    102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      |  -         -    |  272       282       292       302       312       322       332       342       352       362   
                                                                                                                   91  95                                                                                                                                                       249               267
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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, 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 3R5F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3R5F)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5H614_XANOR | Q5H614)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008716    D-alanine-D-alanine ligase activity    Catalysis of the reaction: 2 D-alanine + ATP = D-alanyl-D-alanine + ADP + 2 H(+) + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  3r5f
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  Q5H614_XANOR | Q5H614
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 Related Entries

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

UniProtKB/TrEMBL
        Q5H614_XANOR | Q5H614: 4l1k 4me6

(-) Related Entries Specified in the PDB File

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