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(-) Description

Title :  STRUCTURE OF RUVB COMPLEXED WITH RUVA DOMAIN III
 
Authors :  K. Yamada, T. Miyata, D. Tsuchiya, T. Oyama, Y. Fujiwara, T. Ohnishi, H. Iwasaki, H. Shinagawa, M. Ariyoshi, K. Mayanagi, K. Morikawa
Date :  04 Jul 02  (Deposition) - 06 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Heterodimeric Protein Complex, Aaa-Atpase Domain, Complex With Nucleotide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Yamada, T. Miyata, D. Tsuchiya, T. Oyama, Y. Fujiwara, T. Ohnishi, H. Iwasaki, H. Shinagawa, M. Ariyoshi, K. Mayanagi, K. Morikawa
Crystal Structure Of The Ruva-Ruvb Complex: A Structural Basis For The Holliday Junction Migrating Motor Machinery
Mol. Cell V. 10 671 2002
PubMed-ID: 12408833  |  Reference-DOI: 10.1016/S1097-2765(02)00641-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOLLIDAY JUNCTION DNA HELICASE RUVA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RUVA DOMAIN III
    Gene: RUVA
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274
 
Molecule 2 - RUVB
    Chains: B
    EC Number: 3.6.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-318
    Gene: RUVB
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG B:7 , TYR B:14 , ILE B:15 , GLY B:50 , LYS B:51 , THR B:52 , THR B:53 , TYR B:168 , MET B:204 , ARG B:205 , LYS B:208BINDING SITE FOR RESIDUE ANP B 319

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IXS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IXS)

(-) 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:50
 aligned with RUVA_THET8 | Q9F1Q3 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:50
                                   151       161       171       181       191
           RUVA_THET8   142 ESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALKRLR 191
               SCOP domains d1ixsa_ A:                                         SCOP domains
               CATH domains 1ixsA00 A:142-191                                  CATH domains
               Pfam domains -------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------- Transcript
                 1ixs A 142 ESEAAEEAVMALAALGFKEAQARAVVLDLLAQNPKARAQDLIKEALKRLR 191
                                   151       161       171       181       191


Chain B from PDB  Type:PROTEIN  Length:315
 aligned with RUVB_THET8 | Q5SL87 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:315
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313     
           RUVB_THET8     4 LALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDELGLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVATELAYRHLGYPPPV 318
               SCOP domains d1ixsb2 B:4-242 Holliday junction helicase RuvB                                                                                                                                                                                                d1ixsb1 B:243-318 Holliday junction helicase RuvB                            SCOP domains
               CATH domains 1ixsB01 B:4-167 P-loop containing nucleotide triphosphate hydrolases                                                                                                1ixsB02 B:168-243  [code=1.10.8.60, no name defined]                        1ixsB03 B:244-318 'winged helix' repressor DNA binding domain               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..hhhhhhhhhhhhhhhh........eeee.....hhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhheeeee........eeeee....eeeeee.......hhhhhhh.eeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh......hhhhhhhhhh...........hhhhhhhhh.........hhhhhhhh..eee....eeehhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixs B   4 LALRPKTLDEYIGQERLKQKLRVYLEAAKARKEPLEHLLLFGPPGLGKTTLAHVIAHELGVNLRVTSGPAIEKPGDLAAILANSLEEGDILFIDEIHRLSRQAEEHLYPAMEDFVMDIVIGQGPAARTIRLELPRFTLIGATTRPGLITAPLLSRFGIVEHLEYYTPEELAQGVMRDARLLGVRITEEAALEIGRRSRGTMRVAKRLFRRVRDFAQVAGEEVITRERALEALAALGLDELGLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRTPRGRVATELAYRHLGYPPPV 318
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 24)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RUVA_THET8 | Q9F1Q3)
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:0003678    DNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA helix.
    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.
cellular component
    GO:0009379    Holliday junction helicase complex    A DNA helicase complex that forms part of a Holliday junction resolvase complex, where the helicase activity is involved in the migration of the junction branch point. The best-characterized example is the E. coli RuvAB complex, in which a hexamer of RuvB subunits possesses helicase activity that is modulated by association with RuvA.

Chain B   (RUVB_THET8 | Q5SL87)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        RUVA_THET8 | Q9F1Q3: 1ixr
        RUVB_THET8 | Q5SL87: 1hqc 1ixr

(-) Related Entries Specified in the PDB File

1hqc 1HQC CONTAINS RUVB ALONE.
1ixr 1IXR CONTAINS RUVB COMPLEXED WITH RUVA.