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 :  C-TERMINAL DOMAIN OF ESCHERICHIA COLI TOPOISOMERASE I
 
Authors :  L. Yu, C. -X. Zhu, Y. -C. Tse-Dinh, S. W. Fesik
Date :  02 Mar 95  (Deposition) - 08 Mar 96  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (26x)
Keywords :  Gene-Regulating Protein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Yu, C. X. Zhu, Y. C. Tse-Dinh, S. W. Fesik
Solution Structure Of The C-Terminal Single-Stranded Dna-Binding Domain Of Escherichia Coli Topoisomerase I.
Biochemistry V. 34 7622 1995
PubMed-ID: 7779808  |  Reference-DOI: 10.1021/BI00023A008
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TOPOISOMERASE I
    Chains: A
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Gene: C-TERMINAL FRAGMENT OF ESCHERICHIA COLI TOPOISOMERASE I
    Expression System Plasmid: PJW312
    Expression System Taxid: 562
    Fragment: 122 C-TERMINAL RESIDUES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: DH5AI

 Structural Features

(-) Chains, Units

  
NMR Structure (26x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YUA)

(-) Sites  (0, 0)

(no "Site" information available for 1YUA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 26)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26Phe A:43 -Pro A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YUA)

(-) 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:122
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:122
                                   753       763       773       783       793       803       813       823       833       843       853       863  
           TOP1_ECOLI   744 RNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVEGKK 865
               SCOP domains d1yuaa1 A:1-65                                                   d1yuaa2 A:66-122                                          SCOP domains
               CATH domains 1yuaA01 A:1-64 Bacterial Topoisomerase I, domain 1              1yuaA02 A:65-122  [code=2.20.25.10, no name defined]       CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------Topo_Zn_Ribbon-1yuaA01 A:81-122            Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------Topo_Zn_Ribbon-1yuaA02 A:81-122            Pfam domains (2)
         Sec.struct. author ............eeee.........eeeeeee..eeeeee........eee.hhhhhhh.........hhhhh..........eeeeeee..eeeeeee........eeeeee..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yua A   1 MNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVEGKK 122
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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, 2)

NMR Structure
(-)
Class: Small proteins (3458)

(-) CATH Domains  (2, 2)

NMR Structure
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: Zn_Beta_Ribbon (109)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (TOP1_ECOLI | P06612)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003916    DNA topoisomerase activity    Catalysis of the transient cleavage and passage of individual DNA strands or double helices through one another, resulting a topological transformation in double-stranded DNA.
    GO:0003917    DNA topoisomerase type I activity    Catalysis of a DNA topological transformation by transiently cleaving one DNA strand at a time to allow passage of another strand; changes the linking number by +1 per catalytic cycle.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006265    DNA topological change    The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.
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: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 1yua)
 
  Sites
(no "Sites" information available for 1yua)
 
  Cis Peptide Bonds
    Phe A:43 - Pro A:44   [ RasMol ]  
 

(-) 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
  1yua
    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
  TOP1_ECOLI | P06612
    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)
  5.99.1.2
    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
  TOP1_ECOLI | P06612
    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
        TOP1_ECOLI | P06612: 1cy0 1cy1 1cy2 1cy4 1cy6 1cy7 1cy8 1cy9 1cyy 1ecl 1mw8 1mw9 3pwt 3px7 4rul

(-) Related Entries Specified in the PDB File

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