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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX BETWEEN H365R MUTANT OF 67 KDA N-TERMINAL FRAGMENT OF E. COLI DNA TOPOISOMERASE I AND 5'-ACTTCGGGATG-3'
 
Authors :  K. Perry, A. Mondragon
Date :  27 Sep 02  (Deposition) - 14 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  X,Y
Keywords :  Dna Topoisomerase, Decatenase Enzyme, Toprim Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Perry, A. Mondragon
Structure Of A Complex Between E. Coli Dna Topoisomerase I And Single-Stranded Dna.
Structure V. 11 1349 2003
PubMed-ID: 14604525  |  Reference-DOI: 10.1016/J.STR.2003.09.013
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*CP*TP*TP*CP*GP*GP*GP*AP*TP*G)-3'
    Chains: Y
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - DNA TOPOISOMERASE I
    Chains: X
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: 67 KDA N-TERMINAL FRAGMENT
    Gene: TOPA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: OMEGA-PROTEIN, RELAXING ENZYME, UNTWISTING ENZYME, SWIVELASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : XY

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2TMP1Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS X:28 , SER X:29 , LYS X:251 , HOH X:1338BINDING SITE FOR RESIDUE SO4 X 2002
2AC2SOFTWARETRP X:560 , LYS X:561 , HOH X:1041 , HOH X:1138 , HOH X:1231BINDING SITE FOR RESIDUE SO4 X 2004
3AC3SOFTWAREARG X:515 , ARG X:516 , HOH X:1257BINDING SITE FOR RESIDUE SO4 X 2005
4AC4SOFTWAREARG X:202 , ALA X:458 , ARG X:535 , ASN X:539 , HOH X:1043 , HOH X:1252 , HOH X:1429BINDING SITE FOR RESIDUE SO4 X 2007
5AC5SOFTWAREHIS X:469 , LYS X:472 , HOH X:1512BINDING SITE FOR RESIDUE SO4 X 2008
6AC6SOFTWAREASP X:113 , ARG X:114 , GLU X:115 , ARG X:161 , GLN X:165 , ARG X:168 , ARG X:365 , SER X:495 , ALA X:554 , HOH X:1092 , HOH X:1139 , HOH X:1271 , HOH X:1345 , HOH X:1373 , HOH X:1405 , HOH X:1433 , HOH X:1477BINDING SITE FOR RESIDUE TMP X 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MW8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MW8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MW8)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPRIMPS50880 Toprim domain profile.TOP1_ECOLI3-142  1X:3-142
2TOPOISOMERASE_I_PROKPS00396 Prokaryotic DNA topoisomerase I active site.TOP1_ECOLI309-323  1X:309-323

(-) Exons   (0, 0)

(no "Exon" information available for 1MW8)

(-) 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 X from PDB  Type:PROTEIN  Length:561
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:591
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591 
           TOP1_ECOLI     2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQM 592
               SCOP domains d1mw8x_ X: DNA topoisomerase I, 67K N-te                    rminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1mw8X01 X:2-163  [code=3.40.50.140, no n                    ame defined]                                                                                          1mw8X02 X:164-212,X:474-587                      1mw8X03 X:213-279,X:405-473 Topoisomerase I, domain 3              1mw8X04 X:280-404 Topoisomerase I, domain 4                                                                                  1mw8X03 X:213-279,X:405-473 Topoisom     erase I, domain 3           1mw8X02 X:164-212,X:474-587 Topoisomerase I, domain 2                                                             ----- CATH domains
               Pfam domains --Toprim-1mw8X01 X:4-142                                                                                                                     -------------Topoisom_bac-1mw8X02 X:156-565                                                                                                                                                                                                                                                                                                                                                                                            --------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhh.....eeeee.....ee.....--------------------hhhhhhhhhhh...........ee...hhhhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhh.eee......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeeeee..ee....hhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh.........-----.............hhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeeehhhhhhh..-----............eeeeeeeeeeeee.......hhhhhhhhhhhh............hhhhhh..eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TOPRIM  PDB: X:3-142 UniProt: 3-142                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mw8 X   2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSG--------------------DERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYAS-----EAREAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPA-----EDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENNLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQM 592
                                    11        21        31        41         -         -|       71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351     |   - |     371       381       391       401       411       421       431        |-    |  451       461       471       481       491       501       511       521       531       541       551       561       571       581       591 
                                                                  41                   62                                                                                                                                                                                                                                                                                                    357   363                                                                          440   446                                                                                                                                                  


Chain Y from PDB  Type:DNA  Length:7
                                       
                 1mw8 Y 702 CTTCGGG 708
   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)

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

(-) CATH Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Toprim-like (19)
(-)
Clan: no clan defined [family: Topoisom_bac] (8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (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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 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 1mw9 1yua 3pwt 3px7 4rul

(-) Related Entries Specified in the PDB File

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