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Asym./Biol. Unit (Jmol Viewer)

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Title :   COMPLEX OF E.COLI DNA TOPOISOMERASE I WITH 3'-5'-ADENOSINE DIPHOSPHATE

Authors :   H. Feinberg, A. Changela, A. Mondragon

Date :   31 Aug 99 (Deposition) - 08 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Topoisomerase, Relaxing Enzyme, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Feinberg, A. Changela, A. Mondragon
Protein-Nucleotide Interactions In E. Coli Dna Topoisomeras I.
Nat. Struct. Biol. V. 6 961 1999
PubMed-ID: 10504732 | Reference-DOI: 10.1038/13333

Molecule 1 - DNA TOPOISOMERASE I
	Chains	:	A
	EC Number	:	5.99.1.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	67 KDA N-TERMINAL FRAGMENT OF E.COLI TOPOISOMERASE I
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	A3P	1	Ligand/Ion	ADENOSINE-3'-5'-DIPHOSPHATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:340 , ASP A:341 , LEU A:348 , GLU A:520 , LYS A:521 , MET A:522 , ILE A:525 , HIS A:566 , SER A:569 , HOH A:606 , HOH A:728	BINDING SITE FOR RESIDUE A3P A 605

(no "SS Bond" information available for 1CY0)

(no "Cis Peptide Bond" information available for 1CY0)

(no "SAP(SNP)/Variant" information available for 1CY0)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TOPRIM	PS50880	Toprim domain profile.	TOP1_ECOLI	3-142	1	A:3-142
2	TOPOISOMERASE_I_PROK	PS00396	Prokaryotic DNA topoisomerase I active site.	TOP1_ECOLI	309-323	1	A:309-323

(no "Exon" information available for 1CY0)

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:534
 aligned with TOP1_ECOLI | P06612 from UniProtKB/Swiss-Prot  Length:865

    Alignment length:571
                                    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 
           TOP1_ECOLI     2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFT 572
               SCOP domains d1cy0a_ A: DNA topoisomerase I, 67K N                           -terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1cy0A01 A:2-163  [code=3.40.50.140, n                           o name defined]                                                                                   1cy0A02 A:164-212,A:474-570                      1cy0A03 A:213-279,A:405-473 Topoisomerase I, domain 3              1cy0A04 A:280-404 Topoisomerase I, domain 4                                                                                  1cy0A03 A:213-279,A:405-473 Topois          omerase I, domain 3      1cy0A02 A:164-212,A:474-570 Topoisomerase I, domain 2                                            -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhhh...eeeee.....ee..---------------------------hhhhhhh...........ee...hhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh.hhh.eee......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeeeee..ee....hhhhhhhhhhhhhhh.eeeeeeeeeeeee......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhh...........................hhhhh...hhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeeeeeeeeeeehhhhhhh----------.........eeeeeeeeeeeee.......hhhhhhhhhhhh......hhhhhhhhhhhh..eeee..eeeehhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TOPRIM  PDB: A:3-142 UniProt: 3-142                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1cy0 A   2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLP---------------------------ALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVM----------ILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFT 572
                                    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       361       371       381       391       401       411       421       431      |  -       451       461       471       481       491       501       511       521       531       541       551       561       571 
                                                               38                          66                                                                                                                                                                                                                                                                                                                                                                                 438        449

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Multi-domain proteins (alpha and beta) (2421)

Fold: Prokaryotic type I DNA topoisomerase (18)

Superfamily: Prokaryotic type I DNA topoisomerase (18)

Family: Prokaryotic type I DNA topoisomerase (18)

Protein domain: DNA topoisomerase I, 67K N-terminal domain (12)

Escherichia coli [TaxId: 562] (12)

d1cy0a_

(no "Pfam Domain" information available for 1CY0)

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.

Asymmetric/Biological Unit
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(no "Cis Peptide Bonds" information available for 1cy0)

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	1cy0
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	TOP1_ECOLI \| P06612
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	5.99.1.2
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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
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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
1cy9	CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. MONOCLINIC FORM
1cyy	CRYSTAL STRUCTURE OF THE 30 KDA FRAGMENT OF E. COLI DNA TOPOISOMERASE I. HEXAGONAL FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (4, 4)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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