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(-) Description

Title :  STRUCTURE OF FULL LENGTH TOPOISOMERASE I FROM THERMOTOGA MARITIMA IN MONOCLINIC CRYSTAL FORM
 
Authors :  G. Hansen
Date :  09 Mar 06  (Deposition) - 25 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Topoisomerase, Zinc Ribbon, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Hansen, A. Harrenga, B. Wieland, D. Schomburg, P. Reinemer
Crystal Structure Of Full Length Topoisomerase I From Thermotoga Maritima
J. Mol. Biol. V. 358 1328 2006
PubMed-ID: 16600296  |  Reference-DOI: 10.1016/J.JMB.2006.03.012

(-) Compounds

Molecule 1 - DNA TOPOISOMERASE I
    Chains: A, B
    EC Number: 5.99.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TOPA
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: OMEGA-PROTEIN, RELAXING ENZYME, UNTWISTING ENZYME, SWIVELASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2GAJ)

(-) Sites  (0, 0)

(no "Site" information available for 2GAJ)

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:559 -A:578
2A:561 -A:580
3B:559 -B:578
4B:561 -B:580

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:428 -Pro A:429
2Lys B:428 -Pro B:429

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GAJ)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPOISOMERASE_I_PROKPS00396 Prokaryotic DNA topoisomerase I active site.TOP1_THEMA270-292
 		  2A:270-292
B:270-292
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPOISOMERASE_I_PROKPS00396 Prokaryotic DNA topoisomerase I active site.TOP1_THEMA270-292
 		  1A:270-292
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TOPOISOMERASE_I_PROKPS00396 Prokaryotic DNA topoisomerase I active site.TOP1_THEMA270-292
 		  1-
B:270-292

(-) Exons   (0, 0)

(no "Exon" information available for 2GAJ)

(-) Sequences/Alignments

Asymmetric 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:581
 aligned with TOP1_THEMA | P46799 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:595
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596     
           TOP1_THEMA     7 KYIVVESPAKAKTIKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKRERRKSNAKIQDAHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEMRLSFGKYGFYLKCECGKTRSVKNDEIAVIDDGKIFL 601
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhheeee.....ee.......ee.....ee..ee...hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhh..............hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeeeee..eeeee........hhhhhhhhhh...eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhee....ee.............hhhhhhhhhhhhhhhhhhhhh.--------------............hhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee......eeeeeeeeeeehhhhhh................ee...eeeeeeee.......hhhhhhhhhhhhh.....hhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.........eeeeee.....eeeeeee..eeeee......ee.......eee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I_PROK   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gaj A   7 KYIVVESPAKAKTIKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVG--------------AHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEMRLSFGKYGFYLKCECGKTRSVKNDEIAVIDDGKIFL 601
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316 |       -      |336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596     
                                                                                                                                                                                                                                                                                                                                                 318            333                                                                                                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:581
 aligned with TOP1_THEMA | P46799 from UniProtKB/Swiss-Prot  Length:633

    Alignment length:595
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596     
           TOP1_THEMA     7 KYIVVESPAKAKTIKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVGSKRERRKSNAKIQDAHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEMRLSFGKYGFYLKCECGKTRSVKNDEIAVIDDGKIFL 601
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhh...eeee.....ee.......ee.....ee..ee...hhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhh..............hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeee........hhhhhhhhhh...eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhee....ee.............hhhhhhhhhhhhhhhhhhhhh.--------------............hhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee......eeeeeeeeeeehhhhhh................ee...eeeeeeee.......hhhhhhhhhhhhh.....hhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...........eeeeee.....eeeeeee..eeeee......ee.......eee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I_PROK   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gaj B   7 KYIVVESPAKAKTIKSILGNEYEVFASMGHIIDLPKSKFGVDLEKDFEPEFAVIKGKEKVVEKLKDLAKKGELLIASDMDREGEAIAWHIARVTNTLGRKNRIVFSEITPRVIREAVKNPREIDMKKVRAQLARRILDRIVGYSLSPVLWRNFKSNLSAGRVQSATLKLVCDREREILRFVPKKYHRITVNFDGLTAEIDVKEKKFFDAETLKEIQSIDELVVEEKKVSVKKFAPPEPFKTSTLQQEAYSKLGFSVSKTMMIAQQLYEGVETKDGHIAFITYMRTDSTRVSDYAKEEARNLITEVFGEEYVG--------------AHEAIRPTNVFMTPEEAGKYLNSDQKKLYELIWKRFLASQMKPSQYEETRFVLRTKDGKYRFKGTVLKKIFDGYEKVWKTERNTGEFPFEEGESVKPVVVKIEEQETKPKPRYTEGSLVKEMERLGIGRPSTYASTIKLLLNRGYIKKIRGYLYPTIVGSVVMDYLEKKYSDVVSVSFTAEMEKDLDEVEQGKKTDKIVLREFYESFSSVFDRNDRIVVDFPTNQKCSCGKEMRLSFGKYGFYLKCECGKTRSVKNDEIAVIDDGKIFL 601
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316 |       -      |336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596     
                                                                                                                                                                                                                                                                                                                                                 318            333
   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  (0, 0)

(no "SCOP Domain" information available for 2GAJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GAJ)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TOP1_THEMA | P46799)
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.

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    Lys A:428 - Pro A:429   [ RasMol ]  
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  2gaj
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOP1_THEMA | P46799: 2gai

(-) Related Entries Specified in the PDB File

1d6m CRYSTAL STRUCTURE OF E. COLI TOPOISOMERASE III
1ecl CRYSTAL STRUCTURE OF AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I
1gku CRYSTAL STRUCTURE OF REVERSE GYRASE FROM ARCHAEOGLOBUS FULGIDUS
2gai STRUCTURE OF FULL LENGTH TOPOISOMERASE I FROM THERMOTOGA MARITIMA IN TRICLINIC CRYSTAL FORM