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(-) Description

Title :  TERNARY COMPLEX OF ASFV POL X WITH DNA AND MGDGTP
 
Authors :  W. Wu, M. Su, M. Tsai
Date :  03 Jan 13  (Deposition) - 02 Apr 14  (Release) - 12 Nov 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Dna Polymerase, Asfv Pol X, Nucleotidyl Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. J. Wu, M. I. Su, J. L. Wu, S. Kumar, L. H. Lim, C. W. Wang, F. H. Nelissen, M. C. Chen, J. F. Doreleijers, S. S. Wijmenga, M. D. Tsai
How A Low-Fidelity Dna Polymerase Chooses Non-Watson-Crick From Watson-Crick Incorporation.
J. Am. Chem. Soc. V. 136 4927 2014
PubMed-ID: 24617852  |  Reference-DOI: 10.1021/JA4102375

(-) Compounds

Molecule 1 - REPAIR DNA POLYMERASE X
    ChainsA
    EC Number2.7.7.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET-17B
    Organism ScientificAFRICAN SWINE FEVER VIRUS
    Organism Taxid10497
    SynonymPOL X
 
Molecule 2 - 5'-D(P*GP*GP*CP*GP*AP*AP*GP*CP*CP*GP*GP*GP*TP*GP*CP*GP*AP*A P*GP*CP*AP*CP*(DOC))-3'
    ChainsB
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

NMR Structure (3, 4)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG2Ligand/IonMAGNESIUM ION
NMR Structure * (2, 2)
No.NameCountTypeFull Name
1DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
2DOC1Mod. Nucleotide2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

NMR Structure (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:38 , SER A:39 , ARG A:42 , ASN A:48 , ASP A:49 , ASP A:51 , ASP A:100 , PHE A:102 , HIS A:115 , PHE A:116 , MG A:202 , MG A:203 , DG B:10 , DOC B:23BINDING SITE FOR RESIDUE DGT A 201
2AC2SOFTWAREASP A:49 , ASP A:51 , ASP A:100 , DGT A:201 , MG A:203BINDING SITE FOR RESIDUE MG A 202
3AC3SOFTWAREASP A:49 , ASP A:51 , DGT A:201 , MG A:202BINDING SITE FOR RESIDUE MG A 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M2W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M2W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M2W)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.DPOLX_ASFB738-57  1A:38-57
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DNA_POLYMERASE_XPS00522 DNA polymerase family X signature.DPOLX_ASFB738-57  1A:38-57

(-) Exons   (0, 0)

(no "Exon" information available for 2M2W)

(-) Sequences/Alignments

NMR Structure
   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:174
 aligned with DPOLX_ASFB7 | P42494 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
          DPOLX_ASFB7     1 MLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 174
               SCOP domains d2m2wa_ A: DNA polymerase X                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeeee..eeeeehhhhheeeehhhhh......eeeeeee...hhhhh....eee...eeeeeee...eeeeeeee..eeeeeee.eee..hhhhhhhhhhhhhhhhhhhhhhhhh...eee..eeee..eee.....hhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------DNA_POLYMERASE_X    --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2m2w A   1 MLTLIQGKKIVNHLRSRLAFEYNGQLIKILSKNIVAVGSLRREEKMLNDVDLLIIVPEKKLLKHVLPNIRIKGLSFSVKVCGERKCVLFIEWEKKTYQLDLFTALAEEKPYAIFHFTGPVSYLIRIRAALKKKNYKLNQYGLFKNQTLVPLKITTEKELIKELGFTYRIPKKRL 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    

Chain B from PDB  Type:DNA  Length:23
                                                       
                 2m2w B   1 GGCGAAGCCGGGTGCGAAGCACc  23
                                    10        20  |
                                                 23-DOC

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M2W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M2W)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (DPOLX_ASFB7 | P42494)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003887    DNA-directed DNA polymerase activity    Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPOLX_ASFB7 | P424941jaj 1jqr 2m2t 2m2u 2m2v

(-) Related Entries Specified in the PDB File

2m2t 2m2u 2m2v