Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  E. COLI RECQ HRDC DOMAIN
 
Authors :  D. A. Bernstein, J. L. Keck
Date :  04 Dec 04  (Deposition) - 09 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,D
Keywords :  Recq, Dna-Binding Domain, Hrdc, Helicase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Bernstein, J. L. Keck
Conferring Substrate Specificity To Dna Helicases: Role Of The Recq Hrdc Domain
Structure V. 13 1173 2005
PubMed-ID: 16084389  |  Reference-DOI: 10.1016/J.STR.2005.04.018

(-) Compounds

Molecule 1 - ATP-DEPENDENT DNA HELICASE RECQ
    Chains: A, B, D
    EC Number: 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HRDC DOMAIN
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 15)

Asymmetric/Biological Unit (1, 15)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1WUD)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WUD)

(-) 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:77
 aligned with RECQ_ECOLI | P15043 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:77
                                   539       549       559       569       579       589       599       
           RECQ_ECOLI   530 NYDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEMAEQMPITASEMLSVNGVGMRKLERFGKPFMALIRAHVDGD 606
               SCOP domains d1wuda1 A:530-606 HRDC domain from RecQ helicase                              SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 1wud A 530 NYDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEmAEQmPITASEmLSVNGVGmRKLERFGKPFmALIRAHVDGD 606
                                   539       549       559      |569|      579     | 589      |599       
                                                              566-MSE      |     585-MSE    596-MSE      
                                                                  570-MSE  |                             
                                                                         577-MSE                         


Chain B from PDB  Type:PROTEIN  Length:76
 aligned with RECQ_ECOLI | P15043 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:76
                                   540       550       560       570       580       590       600      
           RECQ_ECOLI   531 YDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEMAEQMPITASEMLSVNGVGMRKLERFGKPFMALIRAHVDGD 606
               SCOP domains d1wudb_ B: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1wud B 531 YDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEmAEQmPITASEmLSVNGVGmRKLERFGKPFmALIRAHVDGD 606
                                   540       550       560     | 570      |580    |  590     | 600      
                                                             566-MSE      |     585-MSE    596-MSE      
                                                                 570-MSE  |                             
                                                                        577-MSE                         


Chain D from PDB  Type:PROTEIN  Length:76
 aligned with RECQ_ECOLI | P15043 from UniProtKB/Swiss-Prot  Length:609

    Alignment length:76
                                   540       550       560       570       580       590       600      
           RECQ_ECOLI   531 YDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEMAEQMPITASEMLSVNGVGMRKLERFGKPFMALIRAHVDGD 606
               SCOP domains d1wudd_ D: automated matches                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -HRDC-1wudD01 D:532-599                                              ------- Pfam domains (1)
           Pfam domains (2) -HRDC-1wudD02 D:532-599                                              ------- Pfam domains (2)
           Pfam domains (3) -HRDC-1wudD03 D:532-599                                              ------- Pfam domains (3)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1wud D 531 YDRKLFAKLRKLRKSIADESNVPPYVVFNDATLIEmAEQmPITASEmLSVNGVGmRKLERFGKPFmALIRAHVDGD 606
                                   540       550       560     | 570      |580    |  590     | 600      
                                                             566-MSE      |     585-MSE    596-MSE      
                                                                 570-MSE  |                             
                                                                        577-MSE
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WUD)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: HRDC-like (19)

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,D   (RECQ_ECOLI | P15043)
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:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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).
    GO:0017116    single-stranded DNA-dependent ATP-dependent DNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, in the presence of single-stranded DNA; drives the unwinding of a DNA helix.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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: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:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    GO:0044237    cellular metabolic process    The chemical reactions and pathways by which individual cells transform chemical substances.
    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:0043590    bacterial nucleoid    The region of a bacterial cell to which the DNA is confined.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0030894    replisome    A multi-component enzymatic machine at the replication fork which mediates DNA replication. Includes DNA primase, one or more DNA polymerases, DNA helicases, and other proteins.
    GO:0017117    single-stranded DNA-dependent ATP-dependent DNA helicase complex    A protein complex that possesses single-stranded DNA-dependent DNA helicase activity.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1wud)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1wud)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wud
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RECQ_ECOLI | P15043
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RECQ_ECOLI | P15043
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RECQ_ECOLI | P15043: 1oyw 1oyy

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1WUD)