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Protein

DNA topoisomerase 4 subunit B

Gene

parE

Organism
Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Topoisomerase IV is essential for chromosome segregation. It relaxes supercoiled DNA. Performs the decatenation events required during the replication of a circular DNA molecule.UniRule annotation2 Publications

Catalytic activityi

ATP-dependent breakage, passage and rejoining of double-stranded DNA.UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation1 Publication, Mn2+UniRule annotation1 Publication, Ca2+UniRule annotation1 PublicationNote: Binds two Mg(2+) per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn(2+) or Ca2+.UniRule annotation1 Publication

Enzyme regulationi

Inhibited by quinolones, such as levofloxacin.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei11 – 111ATPUniRule annotation
Binding sitei51 – 511ATPUniRule annotation
Binding sitei78 – 781ATPUniRule annotation
Binding sitei344 – 3441ATPUniRule annotation
Metal bindingi433 – 4331Magnesium 1; catalyticUniRule annotation1 Publication
Sitei458 – 4581Interaction with DNAUniRule annotation
Sitei461 – 4611Interaction with DNAUniRule annotation
Metal bindingi506 – 5061Magnesium 1; catalyticUniRule annotation1 Publication
Metal bindingi506 – 5061Magnesium 2UniRule annotation1 Publication
Metal bindingi508 – 5081Magnesium 2UniRule annotation1 Publication
Sitei513 – 5131Interaction with DNAUniRule annotation
Sitei629 – 6291Interaction with DNAUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi118 – 1247ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

ATP-binding, DNA-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciSPNE170187:GHGN-854-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 4 subunit BUniRule annotation (EC:5.99.1.3UniRule annotation)
Alternative name(s):
Topoisomerase IV subunit BUniRule annotation
Gene namesi
Name:parEUniRule annotation
Ordered Locus Names:SP_0852
OrganismiStreptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
Taxonomic identifieri170187 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
ProteomesiUP000000585 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Pathology & Biotechi

Chemistry

DrugBankiDB01044. Gatifloxacin.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 647647DNA topoisomerase 4 subunit BPRO_0000145443Add
BLAST

Interactioni

Subunit structurei

Heterotetramer composed of ParC and ParE.UniRule annotation3 Publications

Protein-protein interaction databases

DIPiDIP-48520N.
STRINGi170187.SP_0852.

Structurei

Secondary structure

1
647
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni424 – 4263Combined sources
Beta strandi428 – 4336Combined sources
Helixi435 – 4439Combined sources
Turni447 – 4493Combined sources
Beta strandi450 – 4556Combined sources
Turni462 – 4643Combined sources
Helixi467 – 4715Combined sources
Helixi474 – 48310Combined sources
Helixi488 – 4903Combined sources
Helixi493 – 4953Combined sources
Beta strandi499 – 5046Combined sources
Helixi509 – 52416Combined sources
Helixi527 – 5315Combined sources
Beta strandi535 – 5384Combined sources
Beta strandi542 – 5476Combined sources
Helixi550 – 5523Combined sources
Beta strandi554 – 5585Combined sources
Helixi561 – 57010Combined sources
Beta strandi576 – 5794Combined sources
Helixi583 – 5853Combined sources
Helixi588 – 5958Combined sources
Turni598 – 6003Combined sources
Beta strandi603 – 6075Combined sources
Helixi612 – 62211Combined sources
Helixi627 – 63610Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FOEX-ray4.00C/D404-647[»]
3FOFX-ray4.00C/D404-647[»]
3K9FX-ray2.90C/D404-647[»]
3KSAX-ray3.30C/D404-647[»]
3KSBX-ray3.50C/D404-647[»]
3LTNX-ray3.10C/D404-647[»]
3RADX-ray3.35C/D404-647[»]
3RAEX-ray2.90C/D404-647[»]
3RAFX-ray3.24C/D404-647[»]
4JUOX-ray6.53C1-647[»]
4KOEX-ray3.02C/D404-647[»]
4KPEX-ray3.43C/D404-647[»]
4KPFX-ray3.24C/D404-647[»]
ProteinModelPortaliQ59961.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ59961.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini427 – 541115ToprimUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the type II topoisomerase family. ParE type 2 subfamily.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
KOiK02622.
OMAiRRVSTLM.
OrthoDBiEOG6P334W.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_00939. ParE_type2.
InterProiIPR002288. DNA_gyrase_B_C.
IPR003594. HATPase_C.
IPR005740. ParE.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01058. parE_Gpos. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q59961-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKKEININN YNDDAIQVLE GLDAVRKRPG MYIGSTDGAG LHHLVWEIVD
60 70 80 90 100
NAVDEALSGF GDRIDVTINK DGSLTVQDHG RGMPTGMHAM GIPTVEVIFT
110 120 130 140 150
ILHAGGKFGQ GGYKTSGGLH GVGSSVVNAL SSWLEVEITR DGAVYKQRFE
160 170 180 190 200
NGGKPVTTLK KIGTAPKSKT GTKVTFMPDA TIFSTTDFKY NTISERLNES
210 220 230 240 250
AFLLKNVTLS LTDKRTNEAI EFHYENGVQD FVSYLNEDKE ILTPVLYFEG
260 270 280 290 300
EDNGFQVEVA LQYNDGFSDN ILSFVNNVRT KDGGTHETGL KSAITKVMND
310 320 330 340 350
YARKTGLLKE KDKNLEGSDY REGLAAVLSI LVPEEHLQFE GQTKDKLGSP
360 370 380 390 400
LARPVVDGIV ADKLTFFLME NGELASNLIR KAIKARDARE AARKARDESR
410 420 430 440 450
NGKKNKKDKG LLSGKLTPAQ SKNPAKNELY LVEGDSAGGS AKQGRDRKFQ
460 470 480 490 500
AILPLRGKVV NTAKAKMADI LKNEEINTMI YTIGAGVGAD FSIEDANYDK
510 520 530 540 550
IIIMTDADTD GAHIQTLLLT FFYRYMRPLV EAGHVYIALP PLYKMSKGKG
560 570 580 590 600
KKEEVAYAWT DGELEELRKQ FGKGATLQRY KGLGEMNADQ LWETTMNPET
610 620 630 640
RTLIRVTIED LARAERRVNV LMGDKVEPRR KWIEDNVKFT LEETTVF
Length:647
Mass (Da):71,664
Last modified:September 26, 2001 - v3
Checksum:iB688A526C9A4E7BA
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti166 – 1661P → L in CAA65022 (PubMed:8891124).Curated
Sequence conflicti217 – 2171N → D (PubMed:8763932).Curated
Sequence conflicti217 – 2171N → D (PubMed:8891124).Curated
Sequence conflicti460 – 4601V → I (PubMed:8763932).Curated
Sequence conflicti460 – 4601V → I (PubMed:8891124).Curated
Sequence conflicti568 – 5681R → L in CAA65022 (PubMed:8891124).Curated
Sequence conflicti644 – 6441T → A (PubMed:8763932).Curated
Sequence conflicti644 – 6441T → A (PubMed:8891124).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z67739 Genomic DNA. Translation: CAA91550.2.
AE005672 Genomic DNA. Translation: AAK74981.1.
X95717 Genomic DNA. Translation: CAA65022.1.
PIRiD95098.
RefSeqiNP_345341.1. NC_003028.3.
WP_000037283.1. NZ_AKVY01000001.1.

Genome annotation databases

EnsemblBacteriaiAAK74981; AAK74981; SP_0852.
KEGGispn:SP_0852.
PATRICi19706089. VBIStrPne105772_0891.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z67739 Genomic DNA. Translation: CAA91550.2.
AE005672 Genomic DNA. Translation: AAK74981.1.
X95717 Genomic DNA. Translation: CAA65022.1.
PIRiD95098.
RefSeqiNP_345341.1. NC_003028.3.
WP_000037283.1. NZ_AKVY01000001.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3FOEX-ray4.00C/D404-647[»]
3FOFX-ray4.00C/D404-647[»]
3K9FX-ray2.90C/D404-647[»]
3KSAX-ray3.30C/D404-647[»]
3KSBX-ray3.50C/D404-647[»]
3LTNX-ray3.10C/D404-647[»]
3RADX-ray3.35C/D404-647[»]
3RAEX-ray2.90C/D404-647[»]
3RAFX-ray3.24C/D404-647[»]
4JUOX-ray6.53C1-647[»]
4KOEX-ray3.02C/D404-647[»]
4KPEX-ray3.43C/D404-647[»]
4KPFX-ray3.24C/D404-647[»]
ProteinModelPortaliQ59961.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-48520N.
STRINGi170187.SP_0852.

Chemistry

ChEMBLiCHEMBL2363033.
DrugBankiDB01044. Gatifloxacin.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK74981; AAK74981; SP_0852.
KEGGispn:SP_0852.
PATRICi19706089. VBIStrPne105772_0891.

Phylogenomic databases

eggNOGiCOG0187.
HOGENOMiHOG000075154.
KOiK02622.
OMAiRRVSTLM.
OrthoDBiEOG6P334W.

Enzyme and pathway databases

BioCyciSPNE170187:GHGN-854-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ59961.
PROiQ59961.

Family and domain databases

Gene3Di3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
HAMAPiMF_00939. ParE_type2.
InterProiIPR002288. DNA_gyrase_B_C.
IPR003594. HATPase_C.
IPR005740. ParE.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamiPF00204. DNA_gyraseB. 1 hit.
PF00986. DNA_gyraseB_C. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00418. TPI2FAMILY.
SMARTiSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55874. SSF55874. 1 hit.
SSF56719. SSF56719. 1 hit.
TIGRFAMsiTIGR01058. parE_Gpos. 1 hit.
PROSITEiPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of the parC and parE genes of Streptococcus pneumoniae encoding DNA topoisomerase IV: role in fluoroquinolone resistance."
    Pan X., Fisher M.
    J. Bacteriol. 178:4060-4069(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 7785.
  2. Pan X.
    Submitted (JAN-2000) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 329; 347 AND 351.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC BAA-334 / TIGR4.
  4. "ParC subunit of DNA topoisomerase IV of Streptococcus pneumoniae is a primary target of fluoroquinolones and cooperates with DNA gyrase A subunit in forming resistance phenotype."
    Munoz R., de la Campa A.G.
    Antimicrob. Agents Chemother. 40:2252-2257(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 93-647.
    Strain: D39 / NCTC 7466 / Serotype 2.
  5. "Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target."
    Laponogov I., Veselkov D.A., Sohi M.K., Pan X.S., Achari A., Yang C., Ferrara J.D., Fisher L.M., Sanderson M.R.
    PLoS ONE 2:E301-E301(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBUNIT.
  6. "Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases."
    Laponogov I., Sohi M.K., Veselkov D.A., Pan X.S., Sawhney R., Thompson A.W., McAuley K.E., Fisher L.M., Sanderson M.R.
    Nat. Struct. Mol. Biol. 16:667-669(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 404-647 IN COMPLEX WITH PARC AND DNA, SUBUNIT.
  7. "Structural basis of gate-DNA breakage and resealing by type II topoisomerases."
    Laponogov I., Pan X.S., Veselkov D.A., McAuley K.E., Fisher L.M., Sanderson M.R.
    PLoS ONE 5:E11338-E11338(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 404-647 IN COMPLEX WITH PARC; MAGNESIUM; LEVOFLOXACIN AND DNA, CATALYTIC ACTIVITY, FUNCTION, ENZYME REGULATION, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiPARE_STRPN
AccessioniPrimary (citable) accession number: Q59961
Secondary accession number(s): P77956
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: September 26, 2001
Last modified: April 29, 2015
This is version 111 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.