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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM
 
Authors :  H. Feinberg, C. Lima, A. Mondragon
Date :  31 Aug 99  (Deposition) - 08 Mar 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Topoisomerase, Decatenating Enzyme, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Feinberg, C. D. Lima, A. Mondragon
Conformational Changes In E. Coli Dna Topoisomerase I.
Nat. Struct. Biol. V. 6 918 1999
PubMed-ID: 10504724  |  Reference-DOI: 10.1038/13283

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE I
    Chains: A, B
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: DH5 ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 30 KDA FRAGMENT COMPRISING DOMAINS II AND III
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1CY9)

(-) Sites  (0, 0)

(no "Site" information available for 1CY9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CY9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CY9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CY9)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPOISOMERASE_I_PROKPS00396 Prokaryotic DNA topoisomerase I active site.TOP1_ECOLI309-323
 		  2A:309-323
B:309-323

(-) Exons   (0, 0)

(no "Exon" information available for 1CY9)

(-) 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:245
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:260
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473
           TOP1_ECOLI   214 FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKP 473
               SCOP domains d1cy9a_ A: DNA topoisomerase I, 67K N-terminal domain                                                                                                                                                                                                                SCOP domains
               CATH domains ----1cy9A02 A:218-279,A:405-471 Topoisomerase I, domain 3         1cy9A01 A:280-404 Topoisomerase I, domain 4                                                                                  1cy9A02 A:218-279,A:405-471 Topois        omerase I, domain 3      -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeee.....eeeeeeeee..ee....hhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.........-------...........hhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeeehhhhhh.--------...........eeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------TOPOISOMERASE_I------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cy9 A 214 FVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYAS-------HEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVM--------DRILPAVNKGDALTLVELTPAQHFTKP 473
                                   223       233       243       253       263       273       283       293       303       313       323       333       343       353   |     - |     373       383       393       403       413       423       433    |    -   |   453       463       473
                                                                                                                                                                         357     365                                                                      438      447                          


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:257
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       
           TOP1_ECOLI   216 PEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTK 472
               SCOP domains d1cy9b_ B: DNA topoisomerase I, 67K N-terminal domain                                                                                                                                                                                                             SCOP domains
               CATH domains --1cy9B02 B:218-279,B:405-470 Topoisomerase I, domain 3         1cy9B01 B:280-404 Topoisomerase I, domain 4                                                                                  1cy9B02 B:218-279,B:405-470 Topoiso       merase I, domain 3      -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.....eeeeeeeee..ee....hhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.........-------...........hhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeeehhhhhh..-------...........eeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------TOPOISOMERASE_I----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cy9 B 216 PEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYAS-------HEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMP-------DRILPAVNKGDALTLVELTPAQHFTK 472
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355 |     365       375       385       395       405       415       425       435   |     - |     455       465       
                                                                                                                                                                       357     365                                                                       439     447
   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)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CY9)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

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  TOP1_ECOLI | P06612
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  5.99.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP1_ECOLI | P06612: 1cy0 1cy1 1cy2 1cy4 1cy6 1cy7 1cy8 1cyy 1ecl 1mw8 1mw9 1yua 3pwt 3px7 4rul

(-) Related Entries Specified in the PDB File

1cy0 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE
1cy1 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPT
1cy2 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH TPTPTP3'
1cy4 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'PTPTPTP3'
1cy6 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-THYMIDINE MONOPHOSPHATE
1cy7 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE
1cy8 COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 5'-THYMIDINE MONOPHOSPHATE AND 3'- THYMIDINE MONOPHOSPHATE
1cyy CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM