Q55750 (MFD_SYNY3) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcription-repair-coupling factor
Short name=TRCF
EC=3.6.4.-

Alternative name(s):
ATP-dependent helicase mfd

Gene names

Name:	mfd
Ordered Locus Names:	sll0377

Organism

Synechocystis sp. (strain PCC 6803 / Kazusa) [Reference proteome] [HAMAP]

Taxonomic identifier

1111708 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Cyanobacteria › Oscillatoriophycideae › Chroococcales › Synechocystis › Synechocystis sp. PCC 6803

Protein attributes

Sequence length	1199 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Necessary for strand-specific repair. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognized by TRCF which releases RNAP and the truncated transcript; the TCRF may replace RNAP at the lesion site and then recruit the UvrA/B/C repair system By similarity.
Sequence similarities	In the N-terminal section; belongs to the UvrB family. In the C-terminal section; belongs to the helicase family. RecG subfamily. Contains 1 helicase ATP-binding domain. Contains 1 helicase C-terminal domain.

Ontologies

Keywords
Biological process	DNA damage DNA repair
Ligand	ATP-binding DNA-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA repair Inferred from electronic annotation. Source: UniProtKB-KW
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro damaged DNA binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1199	1199	Transcription-repair-coupling factor		PRO_0000102174
Regions
	Domain	660 – 822	163	Helicase ATP-binding
	Domain	847 – 997	151	Helicase C-terminal
	Nucleotide binding	673 – 680	8	ATP Potential
	Motif	775 – 778	4	DEEQ box

Sequences

	Sequence		Length	Mass (Da)
	Q55750 [UniParc]. Last modified November 1, 1996. Version 1. Checksum: 4D4C32AF60BAC1C9	FASTA	1,199	134,536
	10 20 30 40 50 60 MAEPRAVLKQ GNRNRDKDSV GLGNRLRFVS ISSALNPMTF SSILRHLQTL PLSKDLREKL 70 80 90 100 110 120 QKRGHVQLSG LPRLPKGLIV SSLAQSLEKN LLVITATLEE AGRWTAQLEL MGWQTVNFYP 130 140 150 160 170 180 TSEASPYDPG RLESEMVWGQ MQVLAELIQG HQVKGKAIVA TEKALQPHLP PVATLREYCL 190 200 210 220 230 240 ALRRGQEMDS KSLELTLARL GYERGSTVET EGQWSRRGDI VDIFPVSAEL PVRLEWFGDE 250 260 270 280 290 300 LEKIREFDPA SQRSLDDLTG LVLTPTSFDQ VIEPALNAQA IDLSAWGEDA ETEQLFGKEG 310 320 330 340 350 360 LQRFLGLAFT EPACLLDYLP TETVCVLDEP EQCAAHSERW FEAVAQDWSA LQLPNLPQLH 370 380 390 400 410 420 RNFSALGDRL KTDFQYITLS EIHEANGDSL DISARPIPTM PHQFAKLAEI LRGKREIYSG 430 440 450 460 470 480 LTLGQYSTWL ISAQPSRTVS LLQEHDCAVQ FIANPRDYPA IEKSQIQRTA VTLKYSGLAE 490 500 510 520 530 540 LEGFILPTFR LVLVTDRELF GQHALATPEY VRKRRRATSK QVDINKLSPG DYVVHKSHGI 550 560 570 580 590 600 GKFLKLDALA NREYLMIQYA DGILRVPADS LDSLSRFRHT GTRPPELHKM GGKVWEATKN 610 620 630 640 650 660 KVRKAVKKLA VDLLNLYAKR AKQVGYAYPP DSPWQQELED SFPYQPTPDQ LKAVQDVKRD 670 680 690 700 710 720 LEGDRPMDRL VCGDVGFGKT EVAVRAIFKA VTSGNKQVAL LAPTTVLTQQ HYHTLKERFA 730 740 750 760 770 780 PYPITIGLLN RFRTASEKKE ILAKLKSGEL DIVVGTQQVL GTSVKFKDLG LLVIDEEQRF 790 800 810 820 830 840 GVNQKEKIKT LKTEVDVLTL TATPIPRTLY MSLSGIREMS LITTPPPSRR PIKTHLSPYN 850 860 870 880 890 900 PEVIRTAIRN ELDRGGQVFY VVPRIEGIEE LGGQLRQMVP SARIAIGHGQ MEESELESTM 910 920 930 940 950 960 LAFNDGEADI LVCTTIIEAG LDIPRVNTII VEDAQKFGLA QLYQLRGRVG RSGIQAHAWL 970 980 990 1000 1010 1020 LYPNQKQLTE KARLRLRALQ EFSQLGSGYQ LATRDMEIRG VGNLLGAEQS GQMEAIGYEF 1030 1040 1050 1060 1070 1080 YMEMLQDAIK EIQGQEIPKV EDTQIDLPLT AFIPSDYIPD LEEKMAAYRR ITSIESTDEL 1090 1100 1110 1120 1130 1140 PKIALDWGDR YGMLPSPVEE LFKVVKLKHL AKSLGFSRIK VEGKQNLVLE TPMEEPAWKL 1150 1160 1170 1180 1190 LAENLPNHLQ SRFVYSAKKV VVRGLGVLAP AKQMDNLIDW FGKMQGALPE TKMETLVGK

References

[1]

"Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome." Kaneko T., Tanaka A., Sato S., Kotani H., Sazuka T., Miyajima N., Sugiura M., Tabata S. DNA Res. 2:153-166(1995) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 27184 / PCC 6803 / N-1.

[2]

"Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions." Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S. , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PCC 6803 / Kazusa.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000022 Genomic DNA. Translation: BAA10395.1.
PIR	S76549.
RefSeq	NP_442325.1. NC_000911.1. YP_007452201.1. NC_020286.1.
3D structure databases
ProteinModelPortal	Q55750.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q55750. 4 interactions.
STRING	1148.sll0377.
Proteomic databases
PaxDb	Q55750.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAA10395; BAA10395; BAA10395.
GeneID	14617879. 952468.
KEGG	syn:sll0377.
PATRIC	23842314. VBISynSp132158_2697.
Phylogenomic databases
eggNOG	COG1197.
HOGENOM	HOG000216591.
KO	K03723.
OMA	AINDDYL.
ProtClustDB	CLSK893519.
Enzyme and pathway databases
BioCyc	SSP1148:GJOT-2474-MONOMER.
Family and domain databases
InterPro	IPR003711. CarD-like/TRCF_domain. IPR011545. DNA/RNA_helicase_DEAD/DEAH_N. IPR014001. Helicase_ATP-bd. IPR001650. Helicase_C. IPR004576. Mfd. IPR027417. P-loop_NTPase. IPR005118. Tscpt_repair-coupling_fac_dom. [Graphical view]
Pfam	PF02559. CarD_CdnL_TRCF. 1 hit. PF00270. DEAD. 1 hit. PF00271. Helicase_C. 1 hit. PF03461. TRCF. 1 hit. [Graphical view]
SMART	SM01058. CarD_TRCF. 1 hit. SM00487. DEXDc. 1 hit. SM00490. HELICc. 1 hit. SM00982. TRCF. 1 hit. [Graphical view]
SUPFAM	SSF141259. SSF141259. 1 hit. SSF52540. SSF52540. 3 hits.
TIGRFAMs	TIGR00580. mfd. 1 hit.
PROSITE	PS51192. HELICASE_ATP_BIND_1. 1 hit. PS51194. HELICASE_CTER. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

MFD_SYNY3

Accession

Primary (citable) accession number: Q55750

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 15, 1998
Last sequence update:	November 1, 1996
Last modified:	May 29, 2013
This is version 91 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program