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P34534 (TOP2M_CAEEL) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 118. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Putative DNA topoisomerase 2, mitochondrial
Short name=DNA topoisomerase II
EC=5.99.1.3
Gene names
ORF Names:R05D3.12
OrganismCaenorhabditis elegans [Reference proteome]
Taxonomic identifier6239 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Ecdysozoa › Nematoda › Chromadorea › Rhabditida › Rhabditoidea › Rhabditidae › Peloderinae › Caenorhabditis

Protein attributes

Sequence length1170 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceInferred from homology

General annotation (Comments)

Function

Control of topological states of DNA by transient breakage and subsequent rejoining of DNA strands. Topoisomerase II makes double-strand breaks By similarity.

Catalytic activity

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

Cofactor

Magnesium. Binds two Mg2+ per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ and Ca2+ By similarity.

Subunit structure

Homodimer By similarity.

Subcellular location

Mitochondrion By similarity.

Sequence similarities

Belongs to the type II topoisomerase family.

Contains 1 Toprim domain.

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform a (identifier: P34534-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Note: No experimental confirmation available.
Isoform b (identifier: P34534-2)

The sequence of this isoform differs from the canonical sequence as follows:
     145-1170: Missing.
Note: No experimental confirmation available.
Isoform c (identifier: P34534-3)

The sequence of this isoform differs from the canonical sequence as follows:
     127-1170: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – ?Mitochondrion Potential
Chain? – 1170Putative DNA topoisomerase 2, mitochondrialPRO_0000034819

Regions

Domain475 – 590116Toprim
Nucleotide binding163 – 1653ATP By similarity
Nucleotide binding176 – 1838ATP By similarity
Nucleotide binding396 – 3983ATP By similarity

Sites

Active site8131O-(5'-phospho-DNA)-tyrosine intermediate By similarity
Metal binding4811Magnesium 1; catalytic By similarity
Metal binding5591Magnesium 1; catalytic By similarity
Metal binding5591Magnesium 2 By similarity
Metal binding5611Magnesium 2 By similarity
Binding site1061ATP By similarity
Binding site1351ATP By similarity
Site5091Interaction with DNA By similarity
Site5121Interaction with DNA By similarity
Site6791Interaction with DNA By similarity
Site6801Interaction with DNA By similarity
Site7301Interaction with DNA By similarity
Site7651Interaction with DNA By similarity
Site7711Interaction with DNA By similarity
Site8121Transition state stabilizer By similarity
Site8641Important for DNA bending; intercalates between base pairs of target DNA By similarity

Natural variations

Alternative sequence127 – 11701044Missing in isoform c.
VSP_042232
Alternative sequence145 – 11701026Missing in isoform b.
VSP_042233

Sequences

Sequence LengthMass (Da)Tools
Isoform a [UniParc].

Last modified January 25, 2012. Version 5.
Checksum: E4A72D635186E61E

FASTA1,170133,720
        10         20         30         40         50         60 
MHRLRVLRHL KFCISTSHRT TVVLKNTRSF CNNIPSTSFA SEAAAKYEKK SPTEHVLLRP 

        70         80         90        100        110        120 
DTYIGGVAMR EDQIIWLRDS ENRKMIAKEV TYPPGLLKIF DEILVNAADN KARDSSMNRL 

       130        140        150        160        170        180 
EVWLDRETAR ISVWNNGSGL PVEIHPTEGI YVPTLVFGNL FTSSNYDDSE IKTVGGRNGY 

       190        200        210        220        230        240 
GAKLCNIFSK EFIVETVDTR IKRRFRQKWY DNMKKCNEAE VVEILDETVK DYTKVEFVPD 

       250        260        270        280        290        300 
LERFQIDKLS DDVIDLIGRR VFEVAATLPR DVDVYLNGQK CDVDGFEDYV KMFNDSSSLL 

       310        320        330        340        350        360 
FLHPTPRWHV GVAKRNNFFG ESHVVLPKIV SFVNNINTEK GGSHVDYVMD KIVNIIKPIV 

       370        380        390        400        410        420 
DSKLGDPTKS VKPAVIKNNL SIFINCLIEN PSFESQTKET LTTKAKNFGS IFECDAKKTA 

       430        440        450        460        470        480 
EWAEQSGLIE DIVEEVLNMK KKKLPGKRVS VSSVRDIVKL EDAEWAGITG TAEKCTLILT 

       490        500        510        520        530        540 
EGDSAKALAL AGLEVLGRET YGVFPLKGKL LNVSNLDDAR ASKNEEISNL LRILGLKFED 

       550        560        570        580        590        600 
SNSITRESLR YGRLLILADQ DEDGSHIKGL IVNFIHKFWP SLVHTDGFIQ SFRTPLLKAK 

       610        620        630        640        650        660 
KGDKVRSFFS MNEYRKWADV EEGGKWKIKY YKGLGTSTSN EAREYFSDLD HHTVNFKYTG 

       670        680        690        700        710        720 
TTDDDAIRMA FDRDKSDERK EWIRRSENEI TNEDDGKTEI SYQEFVDGQL MQFGMVDLKR 

       730        740        750        760        770        780 
SIPSLIDGLK PSQRKILWTL LNNMDESTEI KVSQLAGAVA HRQSYHHGEE SLVRTIIRMG 

       790        800        810        820        830        840 
QTFCGSSNLP LLQPIGQFGT RHEGGNDAAS ARYIFTALAP TTRLLFPQAD DDLLQKNVEE 

       850        860        870        880        890        900 
GMVVEPTWLC PIVPLILING TEGIGTGWST KIANRNPIDI IDMIRRKIDS ISTEYEIPPF 

       910        920        930        940        950        960 
YEEFRGKLEV VTPTKFISSG KIQLIRPERK NASTFSIEIV ELPIGIWTSK YKEKLSKIVE 

       970        980        990       1000       1010       1020 
TLPVLEFSER HTEKRVHFRI TLDRKKSSRF LQKSNSDLLN YFKLRTSLTE NRVLFDRNGE 

      1030       1040       1050       1060       1070       1080 
LKEFGNISEI AAEFFEVRRD LYEKRLKIQK EECEAKLIYV ENQLNFIEMV TNGTIEIRSM 

      1090       1100       1110       1120       1130       1140 
GRNQLEEKLQ EMGFRVDPMA TIAKNSKKAN YGYLLEMPVS RLTSDEMKRL EERKSRRRTE 

      1150       1160       1170 
LEAAESADWK SVWRSELDKL AEAVGNNRKS

« Hide

Isoform b [UniParc].

Checksum: 9C511B2CC43F1D6B
Show »

FASTA14416,498
Isoform c [UniParc].

Checksum: 88B55C9A7E199429
Show »

FASTA12614,574

References

[1]"2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans."
Wilson R., Ainscough R., Anderson K., Baynes C., Berks M., Bonfield J., Burton J., Connell M., Copsey T., Cooper J., Coulson A., Craxton M., Dear S., Du Z., Durbin R., Favello A., Fraser A., Fulton L. expand/collapse author list , Gardner A., Green P., Hawkins T., Hillier L., Jier M., Johnston L., Jones M., Kershaw J., Kirsten J., Laisster N., Latreille P., Lightning J., Lloyd C., Mortimore B., O'Callaghan M., Parsons J., Percy C., Rifken L., Roopra A., Saunders D., Shownkeen R., Sims M., Smaldon N., Smith A., Smith M., Sonnhammer E., Staden R., Sulston J., Thierry-Mieg J., Thomas K., Vaudin M., Vaughan K., Waterston R., Watson A., Weinstock L., Wilkinson-Sproat J., Wohldman P.
Nature 368:32-38(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
Strain: Bristol N2.
[2]"Genome sequence of the nematode C. elegans: a platform for investigating biology."
The C. elegans sequencing consortium
Science 282:2012-2018(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], ALTERNATIVE SPLICING.
Strain: Bristol N2.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		FO081667 Genomic DNA. Translation: CCD73199.1.
FO081667 Genomic DNA. Translation: CCD73187.1.
FO081667 Genomic DNA. Translation: CCD73195.1.
RefSeqNP_001129839.2. NM_001136367.2.
NP_001254958.1. NM_001268029.1.
NP_741252.2. NM_171214.4.

3D structure databases

ProteinModelPortalP34534.
SMRP34534. Positions 43-410, 452-1157.
ModBaseSearch...

Protein-protein interaction databases

STRING6239.R05D3.1.

Proteomic databases

PaxDbP34534.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaR05D3.12a; R05D3.12a; R05D3.12.
GeneID259522.
KEGGcel:CELE_R05D3.12.
UCSCR05D3.1. c. elegans.

Organism-specific databases

CTD259522.
WormBaseR05D3.12a; CE45903; WBGene00019876.
R05D3.12b; CE31048; WBGene00019876.
R05D3.12c; CE42620; WBGene00019876.

Phylogenomic databases

eggNOGCOG0187.
GeneTreeENSGT00390000016222.
HOGENOMHOG000216693.
InParanoidP34534.
OMAKLEDAEW.

Family and domain databases

Gene3D1.10.268.10. 1 hit.
3.30.1360.40. 1 hit.
3.30.230.10. 1 hit.
3.30.565.10. 1 hit.
3.40.50.670. 1 hit.
3.90.199.10. 1 hit.
InterProIPR024946. Arg_repress_C-like.
IPR003594. HATPase_ATP-bd.
IPR020568. Ribosomal_S5_D2-typ_fold.
IPR014721. Ribosomal_S5_D2-typ_fold_subgr.
IPR001241. Topo_IIA.
IPR002205. Topo_IIA_A/C.
IPR013758. Topo_IIA_A/C_ab.
IPR013757. Topo_IIA_A_a.
IPR013506. Topo_IIA_bsu_dom2.
IPR013759. Topo_IIA_cen_dom.
IPR013760. Topo_IIA_like_dom.
IPR018522. TopoIIA_CS.
IPR006171. Toprim_domain.
[Graphical view]
PfamPF00204. DNA_gyraseB. 1 hit.
PF00521. DNA_topoisoIV. 1 hit.
PF02518. HATPase_c. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSPR00418. TPI2FAMILY.
SMARTSM00387. HATPase_c. 1 hit.
SM00433. TOP2c. 1 hit.
SM00434. TOP4c. 1 hit.
[Graphical view]
SUPFAMSSF55874. ATP_bd_ATPase. 1 hit.
SSF54211. Ribosomal_S5_D2-typ_fold. 1 hit.
SSF56719. Topo_IIA_cen. 1 hit.
PROSITEPS00177. TOPOISOMERASE_II. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio891486.

Entry information

Entry nameTOP2M_CAEEL
AccessionPrimary (citable) accession number: P34534
Secondary accession number(s): Q8MQ00
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 25, 2012
Last modified: May 1, 2013
This is version 118 of the entry and version 5 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Relevant documents

Caenorhabditis elegans

Caenorhabditis elegans: entries, gene names and cross-references to WormBase

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents