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(-) Description

Title :  DNA POLYMERASE X FROM THERMUS THERMOPHILUS HB8 TERNARY COMPLEX WITH PRIMER/TEMPLATE DNA AND DDGTP
 
Authors :  S. Nakane, R. Masui, S. Kuramitsu
Date :  28 Jan 11  (Deposition) - 25 Jan 12  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym./Biol. Unit :  A,P,T
Keywords :  Rsgi, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Polxc Domain, Php Domain, Dna Polymerase, Drp Lyase, Ap Endonuclease, Dna Repair, Dna Binding, Nucleotide Binding, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Nakane, H. Ishikawa, N. Nakagawa, S. Kuramitsu, R. Masui
The Structural Basis Of The Kinetic Mechanism Of A Gap-Filling X-Family Dna Polymerase That Binds Mg(2+)-Dntp Before Binding To Dna.
J. Mol. Biol. V. 417 179 2012
PubMed-ID: 22306405  |  Reference-DOI: 10.1016/J.JMB.2012.01.025

(-) Compounds

Molecule 1 - DNA POLYMERASE BETA FAMILY (X FAMILY)
    Chains: A
    EC Number: 2.7.7.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POLX, TTHA1150
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
 
Molecule 2 - 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3'
    Chains: P
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3'
    Chains: T
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : APT

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2DDG1Mod. Nucleotide2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE
3DG31Ligand/Ion2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
4MG2Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION
6ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:157 , GLY A:187 , SER A:188 , ARG A:191 , VAL A:196 , GLY A:197 , ASP A:198 , ASP A:200 , TYR A:258 , GLY A:261 , LYS A:263 , ARG A:270 , MG A:577 , MG A:578 , DDG P:7 , DC T:4BINDING SITE FOR RESIDUE DG3 A 576
2AC2SOFTWARESER A:188 , ASP A:198 , ASP A:200 , DG3 A:576BINDING SITE FOR RESIDUE MG A 577
3AC3SOFTWAREASP A:198 , ASP A:200 , ASP A:243 , DG3 A:576BINDING SITE FOR RESIDUE MG A 578
4AC4SOFTWAREGLU A:413 , HIS A:440 , HIS A:468 , ASP A:529BINDING SITE FOR RESIDUE ZN A 579
5AC5SOFTWARELYS A:193BINDING SITE FOR RESIDUE CL A 580
6AC6SOFTWAREARG A:107 , ASP A:426BINDING SITE FOR RESIDUE CL A 581
7AC7SOFTWARELYS A:338BINDING SITE FOR RESIDUE CL A 582
8AC8SOFTWAREHIS A:440 , PHE A:443 , ARG A:477BINDING SITE FOR RESIDUE SO4 A 584

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AU6)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:261 -Ser A:262
2Gly A:383 -Pro A:384
3Pro A:405 -Pro A:406
4Asp A:508 -Leu A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AU6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AU6)

(-) Exons   (0, 0)

(no "Exon" information available for 3AU6)

(-) Sequences/Alignments

Asymmetric/Biological 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:562
 aligned with Q5SJ64_THET8 | Q5SJ64 from UniProtKB/TrEMBL  Length:575

    Alignment length:571
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570 
         Q5SJ64_THET8     1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKA 571
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhh............hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhh.-------..hhhhhhhhhhhhhhhhhhh..ee...hhhhhhhhhhhhhh.........hhhhhh...ee..eeee.......hhhhhhh....eeeeee....eeeeee....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee....eee..eeee..hhhhhhhhh.....hhhhh...hhhhhhh........hhhhh.ee............hhhhhhhhhhhhh..eee..ee......--..hhhhhhhhhhhhhhhhh.....eee.eeee..........hhhhhh...eeee........hhhhhhhhhhhhh......ee................hhhhhhhhhhh...eeeee........hhhhhhhhhh....eeee....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3au6 A   1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDR-------GFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRV--GPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKA 571
                                    10        20        30        40        50        60        70        80        90       100       110       120      |  -    |  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380  |    390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570 
                                                                                                                                                        127     135                                                                                                                                                                                                                                                  380  |                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                                                                                                                                                        383                                                                                                                                                                                            


Chain P from PDB  Type:DNA  Length:7
                                       
                 3au6 P   1 CAGTATg   7
                                  |
                                  7-DDG


Chain T from PDB  Type:DNA  Length:10
                                          
                 3au6 T   2 GGCCATACTG  11
                                    11
   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 3AU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AU6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SJ64_THET8 | Q5SJ64)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

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  Cis Peptide Bonds
    Asp A:508 - Leu A:509   [ RasMol ]  
    Gly A:261 - Ser A:262   [ RasMol ]  
    Gly A:383 - Pro A:384   [ RasMol ]  
    Pro A:405 - Pro A:406   [ RasMol ]  
 

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  2.7.7.7
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 Related Entries

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

UniProtKB/TrEMBL
        Q5SJ64_THET8 | Q5SJ64: 3au2 3auo 3b0x 3b0y

(-) Related Entries Specified in the PDB File

3au2 THE SAME PROTEIN COMPLEXED WITH CA-DGTP RELATED ID: TTK003000748.1 RELATED DB: TARGETDB