Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF HRDC1 DOMAIN OF RECQ HELICASE FROM DEINOCOCCUS RADIODURANS
 
Authors :  S. Liu, W. Zhang, Z. Gao, Q. Ming, H. Hou, W. Lan, H. Wu, C. Cao, Y. Dong
Date :  24 Jun 13  (Deposition) - 10 Jul 13  (Release) - 10 Jul 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
NMR Structure *:  A  (1x)
Keywords :  Dna Binding Protein, Recq Hrdc Domain 1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Liu, W. Zhang, Z. Gao, Q. Ming, H. Hou, W. Lan, H. Wu, C. Cao, Y. Dong
Nmr Structure Of The N-Terminal-Most Hrdc1 Domain Of Recq Helicase From Deinococcus Radiodurans
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA HELICASE RECQ
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET28A
    Fragment: UNP RESIDUES 536-610
    Gene: DRRECQ, DR_1289
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 243230
    Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422

 Structural Features

(-) Chains, Units

  1
NMR Structure : A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MA1)

(-) Sites  (0, 0)

(no "Site" information available for 2MA1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MA1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MA1)

(-) Exons   (0, 0)

(no "Exon" information available for 2MA1)

(-) Sequences/Alignments

NMR Structure
   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:75
 aligned with Q9RUU2_DEIRA | Q9RUU2 from UniProtKB/TrEMBL  Length:824

    Alignment length:75
                                   545       555       565       575       585       595       605     
         Q9RUU2_DEIRA   536 HDAPLFEALRAWRLQKAKELSLPPYTIFHDATLKTIAELRPGSHATLGTVSGVGGRKLAAYGDEVLQVVRDSSGG 610
               SCOP domains d2ma1a_ A: automated matches                                                SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhh......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2ma1 A 536 HDAPLFEALRAWRLQKAKELSLPPYTIFHDATLKTIAELRPGSHATLGTVSGVGGRKLAAYGDEVLQVVRDSSGG 610
                                   545       555       565       575       585       595       605
   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  (1, 1)

NMR Structure
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MA1)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (Q9RUU2_DEIRA | Q9RUU2)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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.
cellular component
    GO:0043590    bacterial nucleoid    The region of a bacterial cell to which the DNA is confined.
    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: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.

 Visualization

(-) Interactive Views

NMR Structure
  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
(no "Ligands, Modified Residues, Ions" information available for 2ma1)
 
  Sites
(no "Sites" information available for 2ma1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ma1)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2ma1
    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
  Q9RUU2_DEIRA | Q9RUU2
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q9RUU2_DEIRA | Q9RUU2
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9RUU2_DEIRA | Q9RUU2: 2rhf 4q47 4q48

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2MA1)