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Asym./Biol. Unit (Jmol Viewer)

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Title :   AMINO TERMINAL 67KDA DOMAIN OF ESCHERICHIA COLI DNA TOPOISOMERASE I (RESIDUES 2-590 OF MATURE PROTEIN) CLONING ARTIFACT ADDS TWO RESIDUES TO THE AMINO-TERMINUS WHICH WERE NOT OBSERVED IN THE EXPERIMENTAL ELECTRON DENSITY (GLY-2, SER-1).

Authors :   C. D. Lima, J. C. Wang, A. Mondragon

Date :   05 May 95 (Deposition) - 31 Jul 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Bacterial Type I, Dna Cleavage, Strand Passage, Topoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. D. Lima, J. C. Wang, A. Mondragon
Three-Dimensional Structure Of The 67K N-Terminal Fragment Of E. Coli Dna Topoisomerase I.
Nature V. 367 138 1994
PubMed-ID: 8114910 | Reference-DOI: 10.1038/367138A0
(for further references see the PDB file header)

Molecule 1 - ESCHERICHIA COLI TOPOISOMERASE I
	Chains	:	A
	EC Number	:	5.99.1.2
	Engineered	:	YES
	Expression System Gene	:	TOPA
	Expression System Plasmid	:	PGEX-2T
	Expression System Vector Type	:	BACTERIAL
	Gene	:	TOPA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ESCHERICHIA COLI OMEGA PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	TY3	AUTHOR	TYR A:319	ACTIVE SITE TYROSINE INVOLVED IN MAKING PHOSPHOTYROSINE COVALENT LINKAGE WITH DNA DURING CATALYSIS

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

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

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

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 1ECL)

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
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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 d1ecla_ A: DNA topoisomerase I, 67K N                       -terminal domain                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1eclA01 A:2-163  [code=3.40.50.140, n                       o name defined]                                                                                       1eclA02 A:164-212,A:474-590                      1eclA03 A:213-279,A:405-473 Topoisomerase I, domain 3              1eclA04 A:280-404 Topoisomerase I, domain 4                                                                                  1eclA03 A:213-279,A:405-473 Topoisome      rase I, domain 3          1eclA02 A:164-212,A:474-590 Topoisomerase I, domain 2                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhh....eeeee.........-----------------------...hhhhhhh..................hhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhh...hhheee.......hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhh.....eeeeeeeeee.....eeeeeeeee.........hhhhhhhhhhhhh..eeeeeeeeeeeee.......hhhhhhhhhhhh...hhhhhhhhhhhhh...............hhhhhhhhhhhhhh..hhh.........--------............hhh.....hhhhhhhhhhhhhhhhhh...eeeeeeeeeeee..eeeeeeeeeeee.hhhh.....------............eeeeeeeeeee........hhhhhhhhhh........hhhhhhhhhh...eeee..eeee.hhhhhhhhhhhhh.hhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -TOPRIM  PDB: A:3-142 UniProt: 3-142                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------------TOPOISOMERASE_I--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ecl A   2 GKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLP-----------------------DERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYA--------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                                                                                                                                                                                                                                                                                                   356      365                                                                         441    448

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( (-)

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Families(

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Protein Domains( (-)

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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)

d1ecla_

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

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
	Complete Structure
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	Ligands, Modified Residues, Ions
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	Sites
		TY3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
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Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
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	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)
Insightii
	ribbon, secondary structure, active site TYR 319 [ mono GIF format \| stereo GIF format ]
	ribbon, sticks, active site TYR 319 [ mono GIF format \| stereo GIF format ]
Midas
	ribbon, secondary structure [ mono GIF format \| stereo GIF format ]
	spacefill, water [ mono GIF format \| stereo GIF format ]
	spacefill, water [ mono GIF format \| stereo GIF format ]
Setor
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	5.99.1.2
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Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (4, 4)

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Gene Ontology (9, 9)

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