4JUO - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   A LOW-RESOLUTION THREE-GATE STRUCTURE OF TOPOISOMERASE IV FROM STREPTOCOCCUS PNEUMONIAE IN SPACE GROUP H32

Authors :   I. Laponogov, D. A. Veselkov, X. -S. Pan, I. Crevel, L. M. Fisher, M. R. Sa

Date :   25 Mar 13 (Deposition) - 28 Aug 13 (Release) - 04 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   6.53

Chains :   Asym./Biol. Unit : A,C,E,F,G,H

Keywords :   Full-Length Pare, Parc55, Open N-Gate, Topoisomerase Iia, Atp Binding, Isomerase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   I. Laponogov, D. A. Veselkov, I. M. Crevel, X. S. Pan, L. M. Fisher, M. R. Sanderson
Structure Of An 'Open' Clamp Type Ii Topoisomerase-Dna Complex Provides A Mechanism For Dna Capture And Transport.
Nucleic Acids Res. V. 41 9911 2013
PubMed-ID: 23965305 | Reference-DOI: 10.1093/NAR/GKT749

Molecule 1 - DNA TOPOISOMERASE 4 SUBUNIT A
	Chains	:	A
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PARC55
	Gene	:	PARC, SP_0855
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	170187
	Strain	:	ATCC BAA-334 / TIGR4
	Synonym	:	TOPOISOMERASE IV SUBUNIT A

Molecule 2 - DNA TOPOISOMERASE 4 SUBUNIT B
	Chains	:	C
	EC Number	:	5.99.1.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	PARE
	Gene	:	PARE
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE SEROTYPE 4
	Organism Taxid	:	170187
	Strain	:	ATCC BAA-334 / TIGR4

Molecule 3 - E-SITE DNA
	Chains	:	E
	Engineered	:	YES
	Synthetic	:	YES

Molecule 4 - E-SITE DNA
	Chains	:	F
	Engineered	:	YES
	Synthetic	:	YES

Molecule 5 - E-SITE DNA
	Chains	:	G
	Engineered	:	YES
	Synthetic	:	YES

Molecule 6 - E-SITE DNA
	Chains	:	H
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	C	E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	LFX	1	Ligand/Ion	(3S)-9-FLUORO-3-METHYL-10-(4-METHYLPIPERAZIN-1-YL)-7-OXO-2,3-DIHYDRO-7H-[1,4]OXAZINO[2,3,4-IJ]QUINOLINE-6-CARBOXYLIC ACID
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	DT E:15 , LFX F:101	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	ASP C:506 , ASP C:508	BINDING SITE FOR RESIDUE MG C 701
3	AC3	SOFTWARE	SER A:79 , MG A:501 , DT E:15 , DA F:1 , DC F:4 , DA F:5 , DT G:15 , DG H:1 , DT H:4 , DA H:5	BINDING SITE FOR RESIDUE LFX F 101

(no "SS Bond" information available for 4JUO)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:168	-	Gly A:169
2	Asp C:37	-	Gly C:38

(no "SAP(SNP)/Variant" information available for 4JUO)

(no "PROSITE Motif" information available for 4JUO)

(no "Exon" information available for 4JUO)

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:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhh........eehhhhhhhhhhhh...hhhhhhhhhhhh..........eeee.................eeeehhhhhhhhhhhhhh...eee......eee.......hhhhhhheeee....eeee...hhhhhhhhhhhhhhh...hhhhhh............eeehhhhhhhhhhhheeeeeee.eeeeee.....eeeeeee.....hhhhhhhhhhhhhhhh....eeeeee........eeeee....hhhhhhhhhhhhh..eeeeeee.eeee..eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4juo A   3 NIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVIVPILSSYIAHRREVILARSRFDKEKAEKRLHIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKKFTPRLSSLED 484
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       343       353       363       373       383       393       403       413       423     ||434       444       454       464       474|        
                                                                                                                                                                                                                                                                                                                                                                           340|                                                                                    429|                                        474|        
                                                                                                                                                                                                                                                                                                                                                                            342                                                                                     431                                         476

Chain C from PDB  Type:PROTEIN  Length:546
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhh......hhhhhhhhhhhhhhhhhhh.eeeeee.....eeeee..hhhhhhh.............hhhhhheeeeeeeeee..eeeeeeee...ee....eeeee......eeeeeeee..........hhhhhhhhhhhhhh.....eeeeee....eeeee....hhhhhhhh.........eeeeeee..eeeeeeeee......eeeeee..ee....hhhhhhhhhhhhhhhhhhhhh........hhhhhh.eeeeeeee...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeeeeehhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhhhhhh...............eeeee...hhhhhhhhhhhhhhhhhhhhhhhhh..eee....ee......hhhhhhh..ee.......hhhhhhhhhh......eeeee..hhhhhhhhhhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4juo C  24 AVRKRPGMYIGSTDGAGLHHLVWEIVDNAVDEALSDRIDVTINKDGSLTVQDHTVEVIFTILHAGGKFLHGVGSSVVNALSSWLEVEITRDGAVYKQRFENGGKPVTTLKKIGTAPKSKTGTKVTFMPDATIFSTTDFKYNTISERLNESAFLLKNVTLSLTDKRTDEAIEFHYEVQDFVSYLNEDKEILTPVLYFEGEDNGFQVEVALQYNDGFSDNILSFVNNVRTKDGGTHETGLKSAITKVMNDYARKTGLLKEKEGSDYREGLAAVLSILVPEEHLQFEGQTKDKLGSPLARPVVDGIVADKLTFFLMENGELASNLIRKAIKARDAREAARKARLTPAQSKNPAKNELYLVEGDSAGGSAKQGRDRKFQAILPLRGKVINTAKAKMADILKNEEINTMIYTIGAGVGADFSIEDANYDKIIIMTDADTDGAHIQTLLLTFFYRYMRPLVEAGHVYIAPPLYKAYAWTDGELEELRKLQRYKGLGEMNADQLWETTMNPETRTLIRVTIEDLARAERRVNVLMGDKVEPRRKWIEDNVKFT 640
                                    33        43        53    ||  66        76  ||   100       120       130       140       150       160       170       180       190       200       210       220    || 232       242       252       262       272       282       292       302       316       326       336       346       356       366       376       386       396|      425       435       445       455       465       475       485       495       505       515       525       535  ||   557       567 ||    584       594       604       614       624       634      
                                                             58|               79|           108|                                                                                                       225|                                                                                311|                                                                             396|                                                                                                                       538| 544|          569|                                                               
                                                              62                94            119                                                                                                        228                                                                                 316                                                                              416                                                                                                                        540  556           577

Chain E from PDB  Type:DNA  Length:7
                                       
                 4juo E   9 CATGAAT  15

Chain F from PDB  Type:DNA  Length:11
                                           
                 4juo F   1 AGTCATTCATG  11
                                    10

Chain G from PDB  Type:DNA  Length:7
                                       
                 4juo G   9 CGTGCAT  15

Chain H from PDB  Type:DNA  Length:11
                                           
                 4juo H   1 GACTATGCACG  11
                                    10

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 '\|'

(no "SCOP Domain" information available for 4JUO)

(no "CATH Domain" information available for 4JUO)

(no "Pfam Domain" information available for 4JUO)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp C:37 - Gly C:38	[ RasMol ]
		Thr A:168 - Gly A:169	[ RasMol ]

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	4juo
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2nov	BREAKAGE-REUNION DOMAIN OF S.PNEUMONIAE TOPO IV: CRYSTAL STRUCTURE OF A GRAM-POSITIVE QUINOLONE TARGET
3foe	STRUCTURAL INSIGHT INTO THE QUINOLONE-DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES
3fof	STRUCTURAL INSIGHT INTO THE QUINOLONE-DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES
3k9f	DETAILED STRUCTURAL INSIGHT INTO THE QUINOLONE-DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES
3ksa	DETAILED STRUCTURAL INSIGHT INTO THE DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (CLEAVED FORM)
3ksb	DETAILED STRUCTURAL INSIGHT INTO THE DNA CLEAVAGE COMPLEX OF TYPE IIA TOPOISOMERASES (RE-SEALED FORM)
3ltn	INHIBITOR-STABILIZED TOPOISOMERASE IV-DNA CLEAVAGE COMPLEX (S. PNEUMONIAE)
3rad	QUINOLONE(CLINAFLOXACIN)-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3rae	QUINOLONE(LEVOFLOXACIN)-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
3raf	QUINAZOLINEDIONE-DNA CLEAVAGE COMPLEX OF TYPE IV TOPOISOMERASE FROM S. PNEUMONIAE
4i3h	A THREE-GATE STRUCTURE OF TOPOISOMERASE IV FROM STREPTOCOCCUS PNEUMONIAE (HIGH RESOLUTION, SPACE GROUP P42212)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (15, 23)

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