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Title :   CRYSTAL STRUCTURE OF THE DNAC-SSDNA COMPLEX

Authors :   Y. H. Lo, K. L. Tsai, Y. J. Sun, C. D. Hsiao

Date :   23 Jul 08 (Deposition) - 30 Dec 08 (Release) - 16 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.10

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (3x)

Keywords :   Hydrolase, Dna Replication, Nucleotide-Binding, Dnac, Helicase, Atp-Binding, Hydrolase-Dna Complex (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

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	:	562
	Expression System Vector	:	PET21B
	Organism Scientific	:	GEOBACILLUS KAUSTOPHILUS HTA426
	Organism Taxid	:	235909
	Synonym	:	DNAC

*Molecule 2 - 5'-D(TPTPTPTPTPTPTPTPTP)-3'**
	Chains	:	C
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	SSDT15
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (3x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2VYE)

(no "Site" information available for 2VYE)

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

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

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

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

(no "Exon" information available for 2VYE)

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:425
 aligned with Q5KU75_GEOKA | Q5KU75 from UniProtKB/TrEMBL  Length:454

    Alignment length:433
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438   
        Q5KU75_GEOKA      9 IPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDLRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTVQLAFIKEYNKFVNL  441
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..........hhhhhhhhh......eeeee....hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhhhhh.eeeeeeehhhhh........hhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhh..--.hhhhhhhhhhhhhhh.eeeeee...--.......eeeeeeeeee...----.eeeee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vye A    9 IPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQD--PMMSDLRESGSIEQDADIVAFLYRDD--NKDSENKNIIEIIIAKQRNG----VQLAFIKEYNKFVNL  441
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368   |  |378       388       398 |  |  408       418   |   428       438   
                                                                                                                                                                                                                                                                                                                                                                                                     372  |                      400  |                422  427              
                                                                                                                                                                                                                                                                                                                                                                                                        375                         403

Chain B from PDB  Type:PROTEIN  Length:381
 aligned with Q5KU75_GEOKA | Q5KU75 from UniProtKB/TrEMBL  Length:454

    Alignment length:421
                                    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 ERIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFKNIKDVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGNINAQNLRTGKLTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKRPMMSDLRESGSIEQDADIVAFLYRDDYYNKDSENKNIIEIIIAKQRNGPVGTV  427
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --DnaB-2vyeB03 B:1009-1111                                                                               -------------------------------------------------   ---------------------DnaB_C-2vyeB01 B:1185-1427                                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) --DnaB-2vyeB04 B:1009-1111                                                                               -------------------------------------------------   ---------------------DnaB_C-2vyeB02 B:1185-1427                                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........---hhhhhhhhhhhhhhh...........hhhhhhh........eeeeee....hhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh----------.hhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhh...eeeeehhhhh..........hhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh----....hhhhhhhh.eee.-------------------.eeee.----... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2vye B 1007 ERIPPQSIEAEQAVLGAVFLDPTALTLASERLIPEDFYRAAHQKIFHAMLRVADKGEPVDLVTVTAELAALEQLEEVGGVSYLSELADSVPTAANVEYYARIVEEKSLLRRLIRTATSIAQDGYTREDEIDVLLDEAERKIMEVSQRKHSGAFK---DVLVQTYDNIEMLHNRNGDITGIPTGFTELDRMTSGFQRSDLIIVAARPSVGKTAFALNIAQNVATKTNENVAIFSLEMSAQQLVMRMLCAEGN----------LTPEDWGKLTMAMGSLSNAGIYIDDTPSIRVSDIRAKCRRLKQESGLGMVVIDYLQLIQGSGRNRENRQQEVSEISRSLKALARELEVPVIALSQLSRSVEQRQDKR----DLRESGSIEQDADIVAF-------------------IIAKQR----GTV 1427
                                  1016      1026      1036      1046      1056      1066      1076      1086      1096      1106      1116      1126      1136      1146      1156   |  1166      1176      1186      1196      1206      1216      1226      1236      1246      1256|        - |    1276      1286      1296      1306      1316      1326      1336      1346      1356      1366       | -  |   1386        |-         -      1416   |  1426 
                                                                                                                                                                                  1160   |                                                                                         1257       1268                                                                                                      1374 1379            1395                1415 1420 1425  
                                                                                                                                                                                      1164

Chain C from PDB  Type:DNA  Length:9
                                          
                2vye C 2001 TTTTTTTTT 2009

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 '\|'

(no "SCOP Domain" information available for 2VYE)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: DnaB_C (8)

Geobacillus kaustophilus (2)

1a	DnaB_C-2vyeB01	B:1185-1427
1b	DnaB_C-2vyeB02	B:1185-1427

Clan: no clan defined [family: DnaB] (9)

Family: DnaB (9)

Geobacillus kaustophilus (2)

2a	DnaB-2vyeB03	B:1009-1111
2b	DnaB-2vyeB04	B:1009-1111

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vye)

Biological Unit
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	2vye
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	Q5KU75_GEOKA \| Q5KU75	:	2vyf

2vyf	CRYSTAL STRUCTURE OF THE DNAC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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