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(-) Description

Title :  STRUCTURE OF HUMAN RECQ-LIKE HELICASE IN COMPLEX WITH A DNA SUBSTRATE
 
Authors :  A. C. W. Pike, Y. Zhang, C. Schnecke, A. Chaikuad, T. Krojer, C. D. O. Cooper, F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, O. Gileadi
Date :  30 Oct 09  (Deposition) - 29 Dec 09  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,O,P,Q,R,S,T
Keywords :  Hydrolase-Dna Complex, Nuclear Protein, Hydrolase, Dna Strand Annealing, Dna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. C. W. Pike, Y. Zhang, C. Schnecke, A. Chaikuad, T. Krojer, C. D. O. Cooper, F. Von Delft, C. H. Arrowsmith, J. Weigelt, A. Edwards, C. Bountra, O. Gileadi
Recq1 Helicase-Driven Dna Unwinding, Annealing, And Branch Migration: Insights From Dna Complex Structures
Proc. Natl. Acad. Sci. Usa V. 112 4286 2015
PubMed-ID: 25831490  |  Reference-DOI: 10.1073/PNAS.1417594112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT DNA HELICASE Q1
    ChainsA, B
    EC Number3.6.1.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantR3-PRARE2
    FragmentRESIDUES 49-616
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRECQ LIKE DNA HELICASE, DNA-DEPENDENT ATPASE Q1
 
Molecule 2 - DNA OLIGO (27BP)
    ChainsO, Q, R, T
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES
 
Molecule 3 - 5'-D(*DA DG DC DG DT DC DG DA DG DA DT DC DCP)-3'
    ChainsP, S
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABOPQRST

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2SO44Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:453 , CYS A:471 , CYS A:475 , CYS A:478BINDING SITE FOR RESIDUE ZN A1595
2AC2SOFTWAREGLY A:116 , GLY A:117 , GLY A:118 , LYS A:119 , SER A:120BINDING SITE FOR RESIDUE SO4 A2000
3AC3SOFTWAREGLN A:292 , TYR A:418 , PHE A:420 , GLU A:543BINDING SITE FOR RESIDUE EDO A2001
4AC4SOFTWARECYS B:453 , CYS B:471 , CYS B:475 , CYS B:478BINDING SITE FOR RESIDUE ZN B1595
5AC5SOFTWARETHR B:115 , GLY B:116 , GLY B:117 , GLY B:118 , LYS B:119 , SER B:120BINDING SITE FOR RESIDUE SO4 B2000
6AC6SOFTWAREGLN B:292 , TYR B:418 , GLU B:540 , GLU B:543BINDING SITE FOR RESIDUE EDO B2001
7AC7SOFTWAREARG A:311 , ARG B:311BINDING SITE FOR RESIDUE SO4 B1597
8AC8SOFTWAREARG A:486BINDING SITE FOR RESIDUE SO4 A1596

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:272 -Lys A:273
2Glu B:272 -Lys B:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034679V102IRECQ1_HUMANPolymorphism1065751A/BV102I
2UniProtVAR_051732V372IRECQ1_HUMANPolymorphism2230003A/BV372I
3UniProtVAR_016140K487TRECQ1_HUMANPolymorphism6501A/BK487T
4UniProtVAR_016141D495HRECQ1_HUMANPolymorphism6499A/BD495H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WWY)

(-) 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:530
 aligned with RECQ1_HUMAN | P46063 from UniProtKB/Swiss-Prot  Length:649

    Alignment length:530
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592
          RECQ1_HUMAN    63 SSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFERKNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKIIAHFLIQQYLKEDYSFTAYATISYLKIGPKANLLNNEAHAITMQVTK 592
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhh...eeee.......hhhhhhhhhh...eeeee..hhhhhhhhhhhhhh....eee.......hhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeee.......eeeeeee...hhhhhhhhhhhhhh......eeeee..hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeee............eeeeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhh...........hhhhhh...eeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhh..eeeeeee....eeeeeee.hhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------I-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------T-------H------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwy A  63 SSPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFERKNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKIIAHFLIQQYLKEDYSFTAYATISYLKIGPKANLLNNEAHAITMQVTK 592
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592

Chain B from PDB  Type:PROTEIN  Length:530
 aligned with RECQ1_HUMAN | P46063 from UniProtKB/Swiss-Prot  Length:649

    Alignment length:530
                                    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       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593
          RECQ1_HUMAN    64 SPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFERKNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKIIAHFLIQQYLKEDYSFTAYATISYLKIGPKANLLNNEAHAITMQVTKS 593
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------DEAD-2wwyB03 B:93-264                                                                                                                                                       -------------------------------------------------------------------Helicase_C-2wwyB05 B:332-409                                                  ------------------------------------------------------------------------------RQC-2wwyB01 B:488-592                                                                                    - Pfam domains (1)
           Pfam domains (2) -----------------------------DEAD-2wwyB04 B:93-264                                                                                                                                                       -------------------------------------------------------------------Helicase_C-2wwyB06 B:332-409                                                  ------------------------------------------------------------------------------RQC-2wwyB02 B:488-592                                                                                    - Pfam domains (2)
         Sec.struct. author hhhhhh.....hhhhhhhhhhhhh.......hhhhhhhhhhh...eeee.......hhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhh......eeeehhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhh..hhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeee.......eeeeeee...hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeee..............eeee.....hhhhhhhhhh........eeeeeeehhhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhh............hhhhhh...eeeeehhhhhhhhhhhhhhhhhh....hhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhh..eeeeeee....eeeeeee.hhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------I-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------T-------H-------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wwy B  64 SPAAWNKEDFPWSGKVKDILQNVFKLEKFRPLQLETINVTMAGKEVFLVMPTGGGKSLCYQLPALCSDGFTLVICPLISLMEDQLMVLKQLGISATMLNASSSKEHVKWVHAEMVNKNSELKLIYVTPEKIAKSKMFMSRLEKAYEARRFTRIAVDEVHCCSQWGHDFRPDYKALGILKRQFPNASLIGLTATATNHVLTDAQKILCIEKCFTFTASFNRPNLYYEVRQKPSNTEDFIEDIVKLINGRYKGQSGIIYCFSQKDSEQVTVSLQNLGIHAGAYHANLEPEDKTTVHRKWSANEIQVVVATVAFGMGIDKPDVRFVIHHSMSKSMENYYQESGRAGRDDMKADCILYYGFGDIFRISSMVVMENVGQQKLYEMVSYCQNISKCRRVLMAQHFDEVWNSEACNKMCDNCCKDSAFERKNITEYCRDLIKILKQAEELNEKLTPLKLIDSWMGKGAAKLRVAGVVAPTLPREDLEKIIAHFLIQQYLKEDYSFTAYATISYLKIGPKANLLNNEAHAITMQVTKS 593
                                    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       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593

Chain O from PDB  Type:DNA  Length:5
                                     
                 2wwy O   1 CGGTA   5

Chain P from PDB  Type:DNA  Length:13
                                             
                 2wwy P   1 AGCGTCGAGATCC  13
                                    10   

Chain Q from PDB  Type:DNA  Length:20
                                                    
                 2wwy Q   7 TGGATCTCGACGCTCTCCCT  26
                                    16        26

Chain R from PDB  Type:DNA  Length:3
                                   
                 2wwy R   2 GGT   4

Chain S from PDB  Type:DNA  Length:12
                                            
                 2wwy S   1 AGCGTCGAGATC  12
                                    10  

Chain T from PDB  Type:DNA  Length:18
                                                  
                 2wwy T   9 GATCTCGACGCTCTCCCT  26
                                    18        

   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 2WWY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Family: RQC (4)
1aRQC-2wwyB01B:488-592
1bRQC-2wwyB02B:488-592

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RECQ1_HUMAN | P46063)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043140    ATP-dependent 3'-5' DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 3' to 5'.
    GO:0004003    ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of the DNA helix.
    GO:0008026    ATP-dependent helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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:0036310    annealing helicase activity    Catalysis of the ATP-dependent rewinding of single-stranded DNA (ssDNA) to reform base pairs between strands. Often acts on ssDNA bubbles bound by replication protein A (RPA).
    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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0000733    DNA strand renaturation    The identification and annealing of complementary base pairs in single-strand DNA.
    GO:0000724    double-strand break repair via homologous recombination    The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RECQ1_HUMAN | P460632v1x 4u7d

(-) Related Entries Specified in the PDB File

2v1x CRYSTAL STRUCTURE OF HUMAN RECQ-LIKE DNA HELICASE