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(-) Description

Title :  CRYSTAL STRUCTURE OF COVALENT COMPLEX OF TOPOISOMERASE 1A WITH SUBSTRATE
 
Authors :  Z. Zhang, Y. C. Tse-Dinh, B. Cheng
Date :  09 Dec 10  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Topoisomerase, Isomerase, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. C. Tse-Dinh, Z. Zhang, B. Cheng
Structure Of E. Coli Topoisomerase I Trapped As Covalent Complex Intermediate With Cleaved Dna
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE
    Chains: A
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-595
    Gene: 415337, ECDH1_2375
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI DH1
    Organism Taxid: 536056
    Strain: ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1
 
Molecule 2 - DNA 5'-D(*TP*TP*GP*GP*G)-3'
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA 5'-D(*A*AP*TP*GP*CP*GP*CP*T)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1HG3Ligand/IonMERCURY (II) ION
2PTR1Mod. Amino AcidO-PHOSPHOTYROSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:281 , TYR A:355 , CYS A:401BINDING SITE FOR RESIDUE HG A 596
2AC2SOFTWAREDT B:1 , DT B:2 , DT C:8 , HG C:9BINDING SITE FOR RESIDUE HG B 6
3AC3SOFTWAREHG B:6 , DT C:8BINDING SITE FOR RESIDUE HG C 9

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PX7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PX7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PX7)

(-) PROSITE Motifs  (2, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PX7)

(-) 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:552
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:589
                                    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         
           TOP1_ECOLI     2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPN 590
               SCOP domains d3px7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhh....eeeee.....ee..-----------------------..hhhhhhhhh...........ee...hhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhh.hhh.eee......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeeeeeeee.....eeeeeeeee..ee....hhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh........--------...........hhhhh...hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeeeeehhhhhh....------..........eeeeeeeeeeeee.......hhhhhhhhhhhh......hhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TOPRIM  PDB: A:3-142 UniProt: 3-142                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3px7 A   2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLP-----------------------DERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATNLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITyMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYA--------HEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPAL------RILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPN 590
                                    11        21        31      |  -         -         -|       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       441      |451       461       471       481       491       501       511       521       531       541       551       561       571       581         
                                                               38                      62                                                                                                                                                                                                                                                              319-PTR                              356      365                                                                         441    448                                                                                                                                              


Chain B from PDB  Type:DNA  Length:2
                                  
                 3px7 B   1 TT   2


Chain C from PDB  Type:DNA  Length:7
                                       
                 3px7 C   2 ATGCGCT   8
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 3PX7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PX7)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(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.

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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 1cy9 1cyy 1ecl 1mw8 1mw9 1yua 3pwt 4rul

(-) Related Entries Specified in the PDB File

1cy0 1cy4 1ecl