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

(-) Description

Title :  PURINE REPRESSOR DNA-BINDING DOMAIN DNA BINDING
 
Authors :  A. Nagadoi, S. Morikawa, H. Nakamura, M. Enari, K. Kobayashi, H. Yamamo G. Sampei, K. Mizobuchi, M. A. Schumacher, R. G. Brennan, Y. Nishimura
Date :  08 May 95  (Deposition) - 08 Mar 96  (Release) - 22 Feb 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
NMR Structure *:  A  (1x)
Keywords :  Purine Repressor, Dna-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Nagadoi, S. Morikawa, H. Nakamura, M. Enari, K. Kobayashi, H. Yamamoto, G. Sampei, K. Mizobuchi, M. A. Schumacher, R. G. Brennan, Y. Nishimura
Structural Comparison Of The Free And Dna-Bound Forms Of Th Purine Repressor Dna-Binding Domain.
Structure V. 3 1217 1995
PubMed-ID: 8591032  |  Reference-DOI: 10.1016/S0969-2126(01)00257-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PURINE REPRESSOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System GenePURR
    Expression System PlasmidPAR2156NCOI
    Expression System StrainBL21
    Expression System Taxid511693
    FragmentDNA-BINDING
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 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 1PRU)

(-) Sites  (0, 0)

(no "Site" information available for 1PRU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.PURR_ECOLI2-56  1A:2-56
2HTH_LACI_1PS00356 LacI-type HTH domain signature.PURR_ECOLI4-22  1A:4-22
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LACI_2PS50932 LacI-type HTH domain profile.PURR_ECOLI2-56  1A:2-56
2HTH_LACI_1PS00356 LacI-type HTH domain signature.PURR_ECOLI4-22  1A:4-22

(-) Exons   (0, 0)

(no "Exon" information available for 1PRU)

(-) 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:56
 aligned with PURR_ECOLI | P0ACP7 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:56
                                    10        20        30        40        50      
            PURR_ECOLI    1 MATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKV 56
               SCOP domains d1prua_ A: Purine repressor (PurR), N-terminal domain    SCOP domains
               CATH domains 1pruA00 A:1-56 lambda repressor-like DNA-binding domains CATH domains
               Pfam domains --LacI-1pruA01 A:3-48                           -------- Pfam domains
         Sec.struct. author ...hhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_LACI_2  PDB: A:2-56 UniProt: 2-56                   PROSITE (1)
                PROSITE (2) ---HTH_LACI_1         ---------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------- Transcript
                  1pru A  1 MATIKDVAKRANVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPSAVARSLKV 56
                                    10        20        30        40        50      

   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

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: HTH (544)

(-) Gene Ontology  (8, 8)

NMR Structure(hide GO term definitions)
Chain A   (PURR_ECOLI | P0ACP7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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 1pru)
 
  Sites
(no "Sites" information available for 1pru)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pru)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
Midas
  ribbon, secondary structure
  sticks
  spacefill
Weblab
  ribbon, secondary structure, lines, labeling
  surface, molecular electrostatic coloring
  ribbon, secondary structure, labeling

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pru
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PURR_ECOLI | P0ACP7
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PURR_ECOLI | P0ACP7
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PURR_ECOLI | P0ACP71bdh 1bdi 1dbq 1jfs 1jft 1jh9 1jhz 1pnr 1prv 1qp0 1qp4 1qp7 1qpz 1qqa 1qqb 1vpw 1wet 1zay 2pua 2pub 2puc 2pud 2pue 2puf 2pug

(-) Related Entries Specified in the PDB File

1prv