CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-002347
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DNA topoisomerase 1 
Protein Synonyms/Alias
 DNA topoisomerase I; Omega-protein; Relaxing enzyme; Swivelase; Untwisting enzyme 
Gene Name
 topA 
Gene Synonyms/Alias
 supX; b1274; JW1266 
Created Date
 July 27, 2013 
Organism
 Escherichia coli (strain K12) 
NCBI Taxa ID
 83333 
Lysine Modification
Position
Peptide
Type
References
19AKAKTINKYLGSDYVacetylation[1]
28LGSDYVVKSSVGHIRacetylation[1]
89HYEVLPGKEKVVSELacetylation[1]
97EKVVSELKQLAEKADacetylation[1]
102ELKQLAEKADHIYLAacetylation[1]
144VVFNEITKNAIRQAFacetylation[1, 2]
153AIRQAFNKPGELNIDacetylation[1]
185MVSPLLWKKIARGLSacetylation[1]
244QVTHQNDKPFRPVNKacetylation[1]
251KPFRPVNKEQTQAAVacetylation[1]
263AAVSLLEKARYSVLEacetylation[1]
274SVLEREDKPTTSKPGacetylation[1]
345YISDNFGKKYLPESPacetylation[1]
346ISDNFGKKYLPESPNacetylation[1, 2]
358SPNQYASKENSQEAHacetylation[1]
381NVMAESLKDMEADAQacetylation[1]
389DMEADAQKLYQLIWRacetylation[1]
407ACQMTPAKYDSTTLTacetylation[1]
436LRFDGWTKVMPALRKacetylation[1]
455RILPAVNKGDALTLVacetylation[1]
472TPAQHFTKPPARFSEacetylation[1]
484FSEASLVKELEKRGIacetylation[1, 2, 3]
488SLVKELEKRGIGRPSacetylation[1]
577DFTQQLDKAEKDPEEacetylation[1]
677DSYLIDPKRKLHVCGacetylation[1]
721CGSEMHLKMGRFGKYacetylation[2]
844QQYVSSEKDGKATGWacetylation[1]
859SAFYVDGKWVEGKK*acetylation[1]
Reference
 [1] Acetyl-Phosphate Is a Critical Determinant of Lysine Acetylation in E. coli.
 Weinert BT, Iesmantavicius V, Wagner SA, Schölz C, Gummesson B, Beli P, Nyström T, Choudhary C.
 Mol Cell. 2013 Jul 25;51(2):265-72. [PMID: 23830618]
 [2] Comprehensive profiling of protein lysine acetylation in Escherichia coli.
 Zhang K, Zheng S, Yang JS, Chen Y, Cheng Z.
 J Proteome Res. 2013 Feb 1;12(2):844-51. [PMID: 23294111]
 [3] The diversity of lysine-acetylated proteins in Escherichia coli.
 Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG.
 J Microbiol Biotechnol. 2008 Sep;18(9):1529-36. [PMID: 18852508] 
Functional Description
 Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone. 
Sequence Annotation
 DOMAIN 3 142 Toprim.
 ZN_FING 599 630 C4-type 1.
 ZN_FING 662 689 C4-type 2.
 ZN_FING 711 736 C4-type 3.
 REGION 192 197 Interaction with DNA.
 ACT_SITE 319 319 O-(5'-phospho-DNA)-tyrosine intermediate.
 METAL 9 9 Magnesium 1; catalytic (By similarity).
 METAL 111 111 Magnesium 1; catalytic (Probable).
 METAL 111 111 Magnesium 2 (Probable).
 METAL 113 113 Magnesium 2 (Probable).  
Keyword
 3D-structure; ATP-binding; Complete proteome; DNA-binding; Isomerase; Magnesium; Metal-binding; Nucleotide-binding; Reference proteome; Repeat; Topoisomerase; Zinc; Zinc-finger. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 865 AA 
Protein Sequence
MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK 60
KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA 120
WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS 180
PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH 240
QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG 300
VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN 360
SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF 420
RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA 480
SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY 540
DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP 600
TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR 660
RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL 720
KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF 780
LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV 840
SSEKDGKATG WSAFYVDGKW VEGKK 865 
Gene Ontology
 GO:0005694; C:chromosome; IEA:InterPro.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0003917; F:DNA topoisomerase type I activity; IMP:EcoCyc.
 GO:0003918; F:DNA topoisomerase type II (ATP-hydrolyzing) activity; IEA:InterPro.
 GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
 GO:0022616; P:DNA strand elongation; IMP:EcoCyc.
 GO:0006265; P:DNA topological change; IGI:EcoliWiki. 
Interpro
 IPR000380; Topo_IA.
 IPR003601; Topo_IA_2.
 IPR023406; Topo_IA_AS.
 IPR013497; Topo_IA_cen.
 IPR013824; Topo_IA_cen_sub1.
 IPR013825; Topo_IA_cen_sub2.
 IPR023405; Topo_IA_core_domain.
 IPR003602; Topo_IA_DNA-bd.
 IPR013498; Topo_IA_Znf.
 IPR005733; TopoI_bac-type.
 IPR013263; TopoI_Znr_bac.
 IPR006171; Toprim_domain. 
Pfam
 PF08272; Topo_Zn_Ribbon
 PF01131; Topoisom_bac
 PF01751; Toprim
 PF01396; zf-C4_Topoisom 
SMART
 SM00437; TOP1Ac
 SM00436; TOP1Bc
 SM00493; TOPRIM 
PROSITE
 PS00396; TOPOISOMERASE_I_PROK
 PS50880; TOPRIM 
PRINTS
 PR00417; PRTPISMRASEI.