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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DNAC
 
Authors :  Y. H. Lo, K. L. Tsai, Y. J. Sun, C. D. Hsiao
Date :  23 Jul 08  (Deposition) - 30 Dec 08  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Hydrolase, Dna Replication, Nucleotide-Binding, Dnac, Helicase, Atp-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. H. Lo, K. L. Tsai, Y. J. Sun, W. T. Chen, C. Y. Huang, C. D. Hsiao
The Crystal Structure Of A Replicative Hexameric Helicase Dnac And Its Complex With Single-Stranded Dna.
Nucleic Acids Res. V. 37 804 2009
PubMed-ID: 19074952  |  Reference-DOI: 10.1093/NAR/GKN999

(-) Compounds

Molecule 1 - REPLICATIVE DNA HELICASE
    Chains: A, B
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET21B
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS HTA426
    Organism Taxid: 235909
    Synonym: DNAC

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1AU4Ligand/IonGOLD ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1AU-1Ligand/IonGOLD ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:221 , ASN A:222BINDING SITE FOR RESIDUE AU A1436
2AC2SOFTWAREMET A:249 , ARG A:250 , CYS A:253BINDING SITE FOR RESIDUE AU A1437
3AC3SOFTWARELEU B:1221BINDING SITE FOR RESIDUE AU B2426
4AC4SOFTWAREMET B:1249BINDING SITE FOR RESIDUE AU B2427

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VYF)

(-) Exons   (0, 0)

(no "Exon" information available for 2VYF)

(-) Sequences/Alignments

Asymmetric 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:398
 aligned with Q5KU75_GEOKA | Q5KU75 from UniProtKB/TrEMBL  Length:454

    Alignment length:429
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427         
        Q5KU75_GEOKA      8 RIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDLRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYN  436
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........hhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.................hhhhhh.......eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhh.....------.......hhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhh....eeeeee...----------------...hhhhhh.eeeeee...---------.eeeeeeeee.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vyf A    8 RIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNI------TGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSR----------------ESGSIEQDADIVAFLYRDD---------NIIEIIIAKQRNGPVGTVQLAFIKEYN  436
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257|      267       277       287       297       307       317       327       337       347       357       | -         -    |  387       397  |      -  |    417       427         
                                                                                                                                                                                                                                                                                    258    265                                                                                                 365              382               400       410                          


Chain B from PDB  Type:PROTEIN  Length:377
 aligned with Q5KU75_GEOKA | Q5KU75 from UniProtKB/TrEMBL  Length:454

    Alignment length:420
                                    16        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       336       346       356       366       376       386       396       406       416       426
        Q5KU75_GEOKA      7 ERIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDLRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGT  426
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --DnaB-2vyfB03 B:1009-1111                                                                               --------------------------------------------  ----------------------   --DnaB_C-2vyfB01 B:1185-1426                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) --DnaB-2vyfB04 B:1009-1111                                                                               --------------------------------------------  ----------------------   --DnaB_C-2vyfB02 B:1185-1426                                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...--....hhhhhhhhhhhhhhhhh.---........hhhhhhh.......eeeeee.....hhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhhhh...............hhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhh.....eeeee..---------...hhhhhhhhhhhhhhhhhhh...eeeeee...----------------...hhhhhh...ee..-------------....ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2vyf B 1007 ERIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKH--AFKNIKDVLVQTYDNIEMLHNR---ITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYL---------RENRQQEVSEISRSLKALARELEVPVIALSQLSR----------------ESGSIEQDADIVAFLY-------------IIEIIIAKQRNGPVGT 1426
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146        |- |    1166      1176  |   1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316     |   -     |1336      1346      1356        |-         -     |1386      1396|        -    | 1416      1426
                                                                                                                                                                             1155  |                 1179   |                                                                                                                                       1322      1332                             1365             1382           1397          1411               
                                                                                                                                                                                1158                     1183
   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 2VYF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: DnaB] (9)
(-)
Family: DnaB (9)
(-)
Geobacillus kaustophilus (2)
2aDnaB-2vyfB03B:1009-1111
2bDnaB-2vyfB04B:1009-1111

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q5KU75_GEOKA | Q5KU75)
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: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: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.
    GO:0006269    DNA replication, synthesis of RNA primer    The synthesis of a short RNA polymer, usually 4-15 nucleotides long, using one strand of unwound DNA as a template; the RNA then serves as a primer from which DNA polymerases extend synthesis.
cellular component
    GO:1990077    primosome complex    Any of a family of protein complexes that form at the origin of replication or stalled replication forks and function in replication primer synthesis in all organisms. Early complexes initiate double-stranded DNA unwinding. The core unit consists of a replicative helicase and a primase. The helicase further unwinds the DNA and recruits the polymerase machinery. The primase synthesizes RNA primers that act as templates for complementary stand replication by the polymerase machinery. The primosome contains a number of associated proteins and protein complexes and contributes to the processes of replication initiation, lagging strand elongation, and replication restart.

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  2vyf
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 Related Entries

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

UniProtKB/TrEMBL
        Q5KU75_GEOKA | Q5KU75: 2vye

(-) Related Entries Specified in the PDB File

2vye CRYSTAL STRUCTURE OF THE DNAC-SSDNA COMPLEX