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(-) Description

Title :  K263D MUTANT OF POLX FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH CA-DGTP
 
Authors :  S. Nakane, N. Nakagawa, R. Masui, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Jun 11  (Deposition) - 02 May 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Polxc, Php, Dna Polymerase, Drp Lyase, 3'-5' Exonuclease, Ap Endonuclease, Dna Repair, Nucleotide, Dna, Transferase (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: ROSETTA2/PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: POLX, TTHA1150
    Mutation: YES
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL1Ligand/IonCHLORIDE ION
3DGT1Ligand/Ion2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
4ZN1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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 , LEU A:259 , THR A:260 , GLY A:261 , ASP A:263 , CA A:578 , CA A:579 , HOH A:597 , HOH A:638 , HOH A:689 , HOH A:805 , HOH A:809 , HOH A:876 , HOH A:888 , HOH A:907BINDING SITE FOR RESIDUE DGT A 576
2AC2SOFTWAREGLU A:413 , HIS A:440 , HIS A:468 , ARG A:506 , HOH A:615 , HOH A:894BINDING SITE FOR RESIDUE ZN A 577
3AC3SOFTWAREASP A:198 , ASP A:200 , DGT A:576 , HOH A:638BINDING SITE FOR RESIDUE CA A 578
4AC4SOFTWAREASP A:198 , ASP A:200 , ASP A:243 , DGT A:576 , HOH A:661 , HOH A:689BINDING SITE FOR RESIDUE CA A 579
5AC5SOFTWAREARG A:175 , LEU A:177 , VAL A:180 , HOH A:781BINDING SITE FOR RESIDUE CA A 580
6AC6SOFTWAREMET A:56 , LEU A:58 , VAL A:61BINDING SITE FOR RESIDUE CA A 581
7AC7SOFTWAREARG A:182 , THR A:296 , GLU A:297BINDING SITE FOR RESIDUE CL A 582

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B0Y)

(-) 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 3B0Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B0Y)

(-) Exons   (0, 0)

(no "Exon" information available for 3B0Y)

(-) 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:575
 aligned with Q5SJ64_THET8 | Q5SJ64 from UniProtKB/TrEMBL  Length:575

    Alignment length:575
                                    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 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSKAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKARRGV 575
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhh.....eeeehhhhhh...ee..eeeeee..hhhhhhhhhhh...eeeeeee...eeeeee....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..eeee..eeee..hhhhhhhhh.....hhhhh...hhhhhhhh.......hhhhh.eeeee.........hhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhhhhhhh..eeeeeeeee.........hhhhhh...eeeee.......hhhhhhhhhhhhhh.....ee................hhhhhhhhhhhhh.eeeee........hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b0y A   1 MRNQELARIFEEIGLMSEFLGDNPFRVRAYHQAARTLYDLDTPIEEIAEKGKEALMELPGVGPDLAEKILEFLRTGKVRKHEELSRKVPRGVLEVMEVPGVGPKTARLLYEGLGIDSLEKLKAALDRGDLTRLKGFGPKRAERIREGLALAQAAGKRRPLGAVLSLARSLLEAIRALPGVERAELCGSARRYKDTVGDLDFLVASREGERAVEGFVRLPQVKEVYAKGKERATVFLKNGLQVDLRVVPPESYGAGLQYLTGSDAHSIRLRALAQEKGLKLSEYGVFRGEKRIAGETEEEVYAALGLPWIPPPLREDQGEVEAALEGRLPKLLELPQVKGDLQVHSTYSDGQNTLEELWEAAKTMGYRYLAVTDHSPAVRVAGGPSPEEALKRVGEIRRFNETHGPPYLLAGAEVDIHPDGTLDYPDWVLRELDLVLVSVHSRFNLPKADQTKRLLKALENPFVHVLAHPTARLLGRRAPIEADWEAVFQKAKEKGVAVEIDGYYDRMDLPDDLARMAYGMGLWISLSTDAHQTDHLRFMELAVGTAQRAWIGPERVLNTLDYEDLLSWLKARRGV 575
                                    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
   Legend:   → Mismatch (orange background)
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    → 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 3B0Y)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B0Y)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B0Y)

(-) 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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 Related Entries

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

UniProtKB/TrEMBL
        Q5SJ64_THET8 | Q5SJ64: 3au2 3au6 3auo 3b0x

(-) Related Entries Specified in the PDB File

3au2 WILD TYPE
3b0x RELATED ID: TTK003000748.1 RELATED DB: TARGETDB