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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BINARY COMPLEX OF RECD2 WITH DNA
 
Authors :  K. Saikrishnan, N. Cook, D. B. Wigley
Date :  23 Mar 09  (Deposition) - 16 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,X
Keywords :  Alpha And Beta Protein, Atp-Binding, Nucleotide-Binding, Helicase, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Saikrishnan, B. Powell, N. J. Cook, M. R. Webb, D. B. Wigley
Mechanistic Basis Of 5'-3' Translocation In Sf1B Helicases.
Cell(Cambridge, Mass. ) V. 137 849 2009
PubMed-ID: 19490894  |  Reference-DOI: 10.1016/J.CELL.2009.03.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EXODEOXYRIBONUCLEASE V, SUBUNIT RECD, PUTATIVE
    Atcc: 13939
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 151-715
    Gene: DR_1902, RECD
    Organism Scientific: DEINOCOCCUS RADIODURANS R1
    Organism Taxid: 243230
    Other Details: N-TERMINUS DELETION MUTANT OF RECD2
    Strain: R1 / DSM 20539 / IFO 15346 / LMG 4051 / NCIB 9279
 
Molecule 2 - 5'-D(*TP*TP*TP*TP*TP*T*TP*TP*TP*TP*TP*TP*TP*T)-3'
    Chains: X
    Engineered: YES
    Other Details: SINGLE-STRANDED OLIGO-DT
    Other Details - Source: SYNTHETIC DNA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AX

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3GP8)

(-) Sites  (0, 0)

(no "Site" information available for 3GP8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GP8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GP8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GP8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GP8)

(-) Exons   (0, 0)

(no "Exon" information available for 3GP8)

(-) 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:551
 aligned with RECDL_DEIRA | Q9RT63 from UniProtKB/Swiss-Prot  Length:715

    Alignment length:564
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            715 
                                   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       602       612       622       632       642       652       662       672       682       692       702       712  | 
          RECDL_DEIRA   153 QGLERRLLAGLQGLGLTINQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSEDDSPLFAAEAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPADGAGNDDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKNDYNNEIFNGTLGMVLKAEGARLTVDFDGNVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRAH-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.hhhhhhhhhhhhhhh...eee......-........eeehhhhhhhhhhhhhhhhhhhhh....----.....hhhhhh..hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhh..eeehhhhh.ee..ee...........eeee.hhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhh.....eeee.......hhhhhhhhhhhhhh.....ee....ee.....eee...-----........eeeee..eeee.---.......hhhh.eee..eeehhhhh...eeeeeeeehhhhhhhhhhhhhhhhhhheeeeeeeeehhhhhhhhhhh.......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gp8 A 153 QGLERRLLAGLQGLGLTINQAQRAVKHFGADALDRLEKDLFTLTEVEGIGFLTADKLWQARGGALDDPRRLTAAAVYALQLAGTQAGHSFLPRSRAEKGVVHYTRVTPGQARLAVETAVELGRLSEDDSPLFA-EAAATGEGRIYLPHVLRAEKKLASLIRTLLATPPAD----DDWAVPKKARKGLSEEQASVLDQLAGHRLVVLTGGPGTGKSTTTKAVADLAESLGLEVGLCAPTGKAARRLGEVTGRTASTVHRLLGYGPQGFRHNHLEPAPYDLLIVDEVSMMGDALMLSLLAAVPPGARVLLVGDTDQLPPVDAGLPLLALAQAAPTIKLTQVYRQAAKNPIIQAAHGLLHGEAPAWGDKRLNLTEIEPDGGARRVALMVRELGGPGAVQVLTPMRKGPLGMDHLNYHLQALFNPGEGGVRIAEGEARPGDTVVQTKN-----IFNGTLGMVLKAEGARLTVD---NVVELTGAELFNLQLGYALTVHRAQGSEWGTVLGVLHEAHMPMLSRNLVYTALTRARDRFFSAGSASAWQIAAARQREARNTALLERIRAHL 716
                                   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   |   602       612        |-  |    632       642       652       662       672       682       692       702       712    
                                                                                                                                                              285 |                                322  327                                                                                                                                                                                                                                                                          596   602                621 625                                                                                           
                                                                                                                                                                287                                                                                                                                                                                                                                                                                                                                                                                                                                             


Chain X from PDB  Type:DNA  Length:8
                                        
                 3gp8 X   1 TTTTTTTT   8
   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 3GP8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GP8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GP8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RECDL_DEIRA | Q9RT63)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0043141    ATP-dependent 5'-3' DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; drives the unwinding of the DNA helix in the direction 5' to 3'.
    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:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008094    DNA-dependent ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction requires the presence of single- or double-stranded DNA, and it drives another reaction.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RECDL_DEIRA | Q9RT63: 3e1s 3gpl

(-) Related Entries Specified in the PDB File

3e1s CRYSTAL STRUCTURE OF AN N-TERMINAL TRUNCATION OF DEINOCOCCUS RADIODURANS RECD2 (NATIVE STRUCTURE)
3gpl CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF RECD2 WITH DNA AND ADPNP