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(-) Description

Title :  THERMOTOGA MARITIMA RUVB K64R MUTANT
 
Authors :  C. D. Putnam, S. B. Clancy, H. Tsuruta, J. G. Wetmur, J. A. Tainer
Date :  12 May 01  (Deposition) - 08 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Aaa+-Class Atpase, Winged-Helix Domain, Holliday Junction, Branch Migration, Walker A, Walker B, Sensor 1, Sensor 2, Arginine Finger, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. D. Putnam, S. B. Clancy, H. Tsuruta, S. Gonzalez, J. G. Wetmur, J. A. Tainer
Structure And Mechanism Of The Ruvb Holliday Junction Branch Migration Motor.
J. Mol. Biol. V. 311 297 2001
PubMed-ID: 11478862  |  Reference-DOI: 10.1006/JMBI.2001.4852
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION DNA HELICASE RUVB
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: RUVB
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RUVB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3CO1Ligand/IonCOBALT (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREACT A:601 , HOH A:766 , HOH A:883BINDING SITE FOR RESIDUE CO A 600
2AC2SOFTWAREGLY A:278 , LEU A:279 , GLY A:313 , ARG A:314 , CO A:600 , HOH A:766 , HOH A:883BINDING SITE FOR RESIDUE ACT A 601
3AC3SOFTWARELEU A:19 , ARG A:20 , PRO A:21 , PHE A:27 , ILE A:28 , PRO A:60 , GLY A:61 , LEU A:62 , GLY A:63 , ARG A:64 , THR A:65 , THR A:66 , TYR A:180 , ILE A:188 , PRO A:216 , ARG A:217 , ILE A:220 , HOH A:711 , HOH A:713 , HOH A:715 , HOH A:729BINDING SITE FOR RESIDUE ADP A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IN6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:275 -Pro A:276

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IN6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1IN6)

(-) Exons   (0, 0)

(no "Exon" information available for 1IN6)

(-) 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:300
 aligned with RUVB_THEMA | Q56313 from UniProtKB/Swiss-Prot  Length:334

    Alignment length:313
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
           RUVB_THEMA    17 QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGKTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDIMIGKGPSAKSIRIDIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTPRGRIVTEKAYKHLKYEVP 329
               SCOP domains d1in6a2 A:17-254 Holliday junction helicase RuvB                                                                                                                                                                                              d1in6a1 A:255-329 Holliday junction helicase RuvB                           SCOP domains
               CATH domains 1in6A01 A:17-180 P-loop containing nucleotide triphosphate hydrolases                                                                                               1in6A03 A:181-255  [code=1.10.8.60, no name defined]                       1in6A02 A:256-328 'winged helix' repressor DNA binding domain            - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhh....-------------.....eeeeee.hhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh....hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhhh..eeee..eeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1in6 A  17 QFLRPKSLDEFIGQENVKKKLSLALEAAKMRGEVLDHVLLAGPPGLGRTTLAHIIASELQTNIHVTSGPVLVKQGDMAAILTSLERGDVLFIDEIHRLNKAVEELLYSAIEDFQIDI-------------DIQPFTLVGATTRSGLLSSPLRSRFGIILELDFYTVKELKEIIKRAASLMDVEIEDAAAEMIAKRSRGTPRIAIRLTKRVRDMLTVVKADRINTDIVLKTMEVLNIDDEGLDEFDRKILKTIIEIYRGGPVGLNALAASLGVEADTLSEVYEPYLLQAGFLARTPRGRIVTEKAYKHLKYEVP 329
                                    26        36        46        56        66        76        86        96       106       116       126      |  -         -|      156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326   
                                                                                                                                              133           147
   Legend:   → Mismatch (orange background)
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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/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IN6)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUVB_THEMA | Q56313)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0009378    four-way junction helicase activity    Catalysis of the unwinding of the DNA helix of DNA containing four-way junctions, including Holliday junctions.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0032508    DNA duplex unwinding    The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating a region of unpaired single strands.
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    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:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    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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  RUVB_THEMA | Q56313
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 Related Entries

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

UniProtKB/Swiss-Prot
        RUVB_THEMA | Q56313: 1in4 1in5 1in7 1in8 1j7k

(-) Related Entries Specified in the PDB File

1in4 THERMOTOGA MARITIMA RUVB HOLLIDAY JUNCTION BRANCH MIGRATION MOTOR
1in5 THERMOGOTA MARITIMA RUVB A156S MUTANT
1in7 THERMOTOGA MARITIMA RUVB R170A
1in8 THERMOTOGA MARITIMA RUVB T158V
1j7k THERMOTOGA MARITIMA RUVB P216G MUTANT