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Transcription termination/antitermination protein NusA (N utilization substance protein A) (Transcription termination/antitermination L factor)

 NUSA_ECOLI              Reviewed;         495 AA.
P0AFF6; P03003; Q2M941;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
20-DEC-2005, sequence version 1.
25-OCT-2017, entry version 112.
RecName: Full=Transcription termination/antitermination protein NusA {ECO:0000255|HAMAP-Rule:MF_00945};
AltName: Full=N utilization substance protein A;
AltName: Full=Transcription termination/antitermination L factor;
Name=nusA {ECO:0000255|HAMAP-Rule:MF_00945};
OrderedLocusNames=b3169, JW3138;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6326058; DOI=10.1093/nar/12.7.3333;
Ishii S., Ihara M., Maekawa T., Nakamura Y., Uchida H., Imamoto F.;
"The nucleotide sequence of the cloned nusA gene and its flanking
region of Escherichia coli.";
Nucleic Acids Res. 12:3333-3342(1984).
[2]
SEQUENCE REVISION.
PubMed=3027511; DOI=10.1007/BF00430455;
Saito M., Tsugawa A., Egawa K., Nakamura Y.;
"Revised sequence of the nusA gene of Escherichia coli and
identification of nusA11 (ts) and nusA1 mutations which cause changes
in a hydrophobic amino acid cluster.";
Mol. Gen. Genet. 205:380-382(1986).
[3]
SEQUENCE REVISION, PARTIAL PROTEIN SEQUENCE, INDUCTION, AND
MUTAGENESIS OF ARG-104; GLY-181; LEU-183 AND GLU-212.
PubMed=1847365; DOI=10.1128/jb.173.4.1492-1501.1991;
Ito K., Egawa K., Nakamura Y.;
"Genetic interaction between the beta' subunit of RNA polymerase and
the arginine-rich domain of Escherichia coli nusA protein.";
J. Bacteriol. 173:1492-1501(1991).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[6]
PROTEIN SEQUENCE OF 1-13.
STRAIN=K12 / EMG2;
PubMed=9298646; DOI=10.1002/elps.1150180807;
Link A.J., Robison K., Church G.M.;
"Comparing the predicted and observed properties of proteins encoded
in the genome of Escherichia coli K-12.";
Electrophoresis 18:1259-1313(1997).
[7]
IDENTIFICATION AS L FACTOR, AND INTERACTION WITH N PROTEIN.
PubMed=6154941; DOI=10.1073/pnas.77.4.1991;
Greenblatt J., Li J., Adhya S., Friedman D.I., Baron L.S.,
Redfield B., Kung H.F., Weissbach H.;
"L factor that is required for beta-galactosidase synthesis is the
nusA gene product involved in transcription termination.";
Proc. Natl. Acad. Sci. U.S.A. 77:1991-1994(1980).
[8]
FUNCTION, AND INTERACTION WITH RNA POLYMERASE.
PubMed=6263495; DOI=10.1016/0092-8674(81)90332-9;
Greenblatt J., Li J.;
"Interaction of the sigma factor and the nusA gene protein of E. coli
with RNA polymerase in the initiation-termination cycle of
transcription.";
Cell 24:421-428(1981).
[9]
FUNCTION.
PubMed=6265785; DOI=10.1038/292215a0;
Greenblatt J., McLimont M., Hanly S.;
"Termination of transcription by nusA gene protein of Escherichia
coli.";
Nature 292:215-220(1981).
[10]
INDUCTION BY COLD-SHOCK.
STRAIN=CSH142;
PubMed=8898389; DOI=10.1111/j.1365-2958.1996.tb02582.x;
Jones P.G., Inouye M.;
"RbfA, a 30S ribosomal binding factor, is a cold-shock protein whose
absence triggers the cold-shock response.";
Mol. Microbiol. 21:1207-1218(1996).
[11]
FUNCTION.
STRAIN=K12;
PubMed=6199039; DOI=10.1021/bi00297a004;
Schmidt M.C., Chamberlin M.J.;
"Amplification and isolation of Escherichia coli nusA protein and
studies of its effects on in vitro RNA chain elongation.";
Biochemistry 23:197-203(1984).
[12]
INTERACTION WITH RHO.
PubMed=6096352;
Schmidt M.C., Chamberlin M.J.;
"Binding of rho factor to Escherichia coli RNA polymerase mediated by
nusA protein.";
J. Biol. Chem. 259:15000-15002(1984).
[13]
INDUCTION.
PubMed=2987884; DOI=10.1093/nar/13.9.3371;
Plumbridge J.A., Dondon J., Nakamura Y., Grunberg-Manago M.;
"Effect of NusA protein on expression of the nusA,infB operon in E.
coli.";
Nucleic Acids Res. 13:3371-3388(1985).
[14]
FUNCTION.
STRAIN=K12;
PubMed=2821282; DOI=10.1016/0022-2836(87)90486-4;
Schmidt M.C., Chamberlin M.J.;
"nusA protein of Escherichia coli is an efficient transcription
termination factor for certain terminator sites.";
J. Mol. Biol. 195:809-818(1987).
[15]
SUBUNIT, AND INTERACTION WITH RNA POLYMERASE.
PubMed=1856861; DOI=10.1016/0022-2836(91)90015-X;
Gill S.C., Weitzel S.E., von Hippel P.H.;
"Escherichia coli sigma 70 and NusA proteins. I. Binding interactions
with core RNA polymerase in solution and within the transcription
complex.";
J. Mol. Biol. 220:307-324(1991).
[16]
FUNCTION, AND INTERACTION WITH NASCENT RNA.
PubMed=7536848; DOI=10.1016/S0022-2836(05)80136-6;
Liu K., Hanna M.M.;
"NusA contacts nascent RNA in Escherichia coli transcription
complexes.";
J. Mol. Biol. 247:547-558(1995).
[17]
IDENTIFICATION BY 2D-GEL.
PubMed=9298644; DOI=10.1002/elps.1150180805;
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R.,
Neidhardt F.C.;
"Escherichia coli proteome analysis using the gene-protein database.";
Electrophoresis 18:1243-1251(1997).
[18]
FUNCTION.
STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
PubMed=9139668; DOI=10.1074/jbc.272.19.12265;
Vogel U., Jensen K.F.;
"NusA is required for ribosomal antitermination and for modulation of
the transcription elongation rate of both antiterminated RNA and
mRNA.";
J. Biol. Chem. 272:12265-12271(1997).
[19]
FUNCTION.
PubMed=11719185; DOI=10.1016/S0092-8674(01)00582-7;
Gusarov I., Nudler E.;
"Control of intrinsic transcription termination by N and NusA: the
basic mechanisms.";
Cell 107:437-449(2001).
[20]
SUBCELLULAR LOCATION.
PubMed=17272300; DOI=10.1093/nar/gkl1158;
Watt R.M., Wang J., Leong M., Kung H.F., Cheah K.S., Liu D.,
Danchin A., Huang J.D.;
"Visualizing the proteome of Escherichia coli: an efficient and
versatile method for labeling chromosomal coding DNA sequences (CDSs)
with fluorescent protein genes.";
Nucleic Acids Res. 35:E37-E37(2007).
[21]
FUNCTION IN DNA REPAIR, AND DISRUPTION PHENOTYPE.
PubMed=20696893; DOI=10.1073/pnas.1005203107;
Cohen S.E., Lewis C.A., Mooney R.A., Kohanski M.A., Collins J.J.,
Landick R., Walker G.C.;
"Roles for the transcription elongation factor NusA in both DNA repair
and damage tolerance pathways in Escherichia coli.";
Proc. Natl. Acad. Sci. U.S.A. 107:15517-15522(2010).
[22]
FUNCTION, AND DOMAIN.
PubMed=21922055; DOI=10.4161/trns.2.3.15671;
Burmann B.M., Rosch P.;
"The role of E. coli Nus-factors in transcription regulation and
transcription:translation coupling: From structure to mechanism.";
Transcription 2:130-134(2011).
[23]
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 352-421, AND DOMAIN.
PubMed=15365170; DOI=10.1073/pnas.0405883101;
Bonin I., Muhlberger R., Bourenkov G.P., Huber R., Bacher A.,
Richter G., Wahl M.C.;
"Structural basis for the interaction of Escherichia coli NusA with
protein N of phage lambda.";
Proc. Natl. Acad. Sci. U.S.A. 101:13762-13767(2004).
[24]
STRUCTURE BY NMR OF 351-426, AND DOMAIN.
PubMed=15987884; DOI=10.1110/ps.051372205;
Eisenmann A., Schwarz S., Prasch S., Schweimer K., Rosch P.;
"The E. coli NusA carboxy-terminal domains are structurally similar
and show specific RNAP- and lambdaN interaction.";
Protein Sci. 14:2018-2029(2005).
[25]
STRUCTURE BY NMR OF 424-495.
Prasch S., Schweimer K., Roesch P.;
"structural basis of transcription elongation control: the NusA-aCTD
complex.";
Submitted (JAN-2008) to the PDB data bank.
[26]
STRUCTURE BY NMR OF 1-125.
Jurk M., Schweimer K., Roesch P.;
"Solution structure of the aminoterminal domain of E. coli NusA.";
Submitted (APR-2010) to the PDB data bank.
-!- FUNCTION: Participates in both transcription termination and
antitermination. Involved in a variety of cellular and viral
termination and antitermination processes, such as Rho-dependent
transcriptional termination, intrinsic termination, and phage
lambda N-mediated transcriptional antitermination. Also important
for coordinating the cellular responses to DNA damage by coupling
the processes of nucleotide excision repair and translesion
synthesis to transcription. {ECO:0000255|HAMAP-Rule:MF_00945,
ECO:0000269|PubMed:11719185, ECO:0000269|PubMed:20696893,
ECO:0000269|PubMed:21922055, ECO:0000269|PubMed:2821282,
ECO:0000269|PubMed:6199039, ECO:0000269|PubMed:6263495,
ECO:0000269|PubMed:6265785, ECO:0000269|PubMed:7536848,
ECO:0000269|PubMed:9139668}.
-!- SUBUNIT: Monomer. Binds directly to the core enzyme of the DNA-
dependent RNA polymerase and to nascent RNA. Also interacts with
the termination Rho factor and the phage lambda N protein.
{ECO:0000255|HAMAP-Rule:MF_00945, ECO:0000269|PubMed:1856861,
ECO:0000269|PubMed:6096352, ECO:0000269|PubMed:6154941,
ECO:0000269|PubMed:6263495, ECO:0000269|PubMed:7536848}.
-!- INTERACTION:
Q47155:dinB; NbExp=3; IntAct=EBI-551571, EBI-1037359;
P0A8U6:metJ; NbExp=3; IntAct=EBI-551571, EBI-555272;
P0A7Z4:rpoA; NbExp=7; IntAct=EBI-551571, EBI-544985;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00945,
ECO:0000269|PubMed:17272300}. Note=Colocalizes with nucleoids.
-!- INDUCTION: In response to low temperature. Negatively
autoregulated. Induced by cold shock (42 to 15 degrees Celsius)
(at protein level) (PubMed:8898389). {ECO:0000269|PubMed:1847365,
ECO:0000269|PubMed:2987884, ECO:0000269|PubMed:8898389}.
-!- DOMAIN: The N-terminal region interacts with RNA polymerase. The
central region is composed of 3 RNA binding domains, S1, KH 1 and
KH 2. The C-terminal region contains 2 acidic repeats, AR1 and
AR2, which bind to protein N from phage lambda during
antitermination. {ECO:0000269|PubMed:15365170,
ECO:0000269|PubMed:15987884, ECO:0000269|PubMed:21922055}.
-!- DISRUPTION PHENOTYPE: Mutants are sensitive to DNA-damaging
agents. {ECO:0000269|PubMed:20696893}.
-!- SIMILARITY: Belongs to the NusA family. {ECO:0000255|HAMAP-
Rule:MF_00945}.
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EMBL; X00513; CAA25200.1; -; Genomic_DNA.
EMBL; U18997; AAA57972.1; -; Genomic_DNA.
EMBL; U00096; AAC76203.1; -; Genomic_DNA.
EMBL; AP009048; BAE77215.1; -; Genomic_DNA.
PIR; E65107; FJEC.
RefSeq; NP_417638.1; NC_000913.3.
RefSeq; WP_001031057.1; NZ_LN832404.1.
PDB; 1U9L; X-ray; 1.90 A; A/B=352-421.
PDB; 1WCL; NMR; -; A=351-426.
PDB; 1WCN; NMR; -; A=426-495.
PDB; 2JZB; NMR; -; B=424-495.
PDB; 2KWP; NMR; -; A=1-125.
PDB; 5LM9; X-ray; 2.14 A; A=101-426.
PDB; 5MS0; EM; 9.80 A; M=1-495.
PDBsum; 1U9L; -.
PDBsum; 1WCL; -.
PDBsum; 1WCN; -.
PDBsum; 2JZB; -.
PDBsum; 2KWP; -.
PDBsum; 5LM9; -.
PDBsum; 5MS0; -.
ProteinModelPortal; P0AFF6; -.
SMR; P0AFF6; -.
BioGrid; 4261878; 15.
DIP; DIP-47857N; -.
IntAct; P0AFF6; 45.
MINT; MINT-1220515; -.
STRING; 316385.ECDH10B_3343; -.
SWISS-2DPAGE; P0AFF6; -.
PaxDb; P0AFF6; -.
PRIDE; P0AFF6; -.
EnsemblBacteria; AAC76203; AAC76203; b3169.
EnsemblBacteria; BAE77215; BAE77215; BAE77215.
GeneID; 947682; -.
KEGG; ecj:JW3138; -.
KEGG; eco:b3169; -.
PATRIC; fig|1411691.4.peg.3561; -.
EchoBASE; EB0659; -.
EcoGene; EG10665; nusA.
eggNOG; ENOG4105CHV; Bacteria.
eggNOG; COG0195; LUCA.
HOGENOM; HOG000006394; -.
InParanoid; P0AFF6; -.
KO; K02600; -.
PhylomeDB; P0AFF6; -.
BioCyc; EcoCyc:EG10665-MONOMER; -.
EvolutionaryTrace; P0AFF6; -.
PRO; PR:P0AFF6; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0001000; F:bacterial-type RNA polymerase core enzyme binding; IDA:CAFA.
GO; GO:0000166; F:nucleotide binding; IEA:InterPro.
GO; GO:0019904; F:protein domain specific binding; IPI:CAFA.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0003700; F:transcription factor activity, sequence-specific DNA binding; IEA:InterPro.
GO; GO:0031564; P:transcription antitermination; IMP:EcoliWiki.
GO; GO:0001125; P:transcription termination from bacterial-type RNA polymerase promoter; IDA:CAFA.
Gene3D; 3.30.1480.10; -; 1.
Gene3D; 3.30.300.20; -; 2.
HAMAP; MF_00945_B; NusA_B; 1.
InterPro; IPR010995; DNA_repair_Rad51/TF_NusA_a-hlx.
InterPro; IPR015946; KH_dom-like_a/b.
InterPro; IPR025249; KH_dom_NusA-like.
InterPro; IPR009019; KH_prok-type.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR030842; NusA_bac.
InterPro; IPR036555; NusA_N_sf.
InterPro; IPR022967; S1_dom.
InterPro; IPR003029; S1_domain.
InterPro; IPR013735; TF_NusA_N.
InterPro; IPR010214; Tscrpt_termin_fac_NusA_C_rpt.
InterPro; IPR010213; Tscrpt_termination_fac_NusA.
Pfam; PF13184; KH_5; 1.
Pfam; PF08529; NusA_N; 1.
Pfam; PF00575; S1; 1.
SMART; SM00316; S1; 1.
SUPFAM; SSF47794; SSF47794; 2.
SUPFAM; SSF50249; SSF50249; 1.
SUPFAM; SSF54814; SSF54814; 2.
SUPFAM; SSF69705; SSF69705; 1.
TIGRFAMs; TIGR01953; NusA; 1.
TIGRFAMs; TIGR01954; nusA_Cterm_rpt; 2.
PROSITE; PS50084; KH_TYPE_1; 1.
PROSITE; PS50126; S1; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Direct protein sequencing;
Reference proteome; Repeat; RNA-binding; Stress response;
Transcription; Transcription antitermination;
Transcription regulation; Transcription termination.
CHAIN 1 495 Transcription termination/antitermination
protein NusA.
/FTId=PRO_0000181965.
DOMAIN 135 200 S1 motif. {ECO:0000255|HAMAP-
Rule:MF_00945}.
DOMAIN 230 293 KH 1. {ECO:0000255|HAMAP-Rule:MF_00945}.
DOMAIN 302 368 KH 2. {ECO:0000255|HAMAP-Rule:MF_00945}.
REPEAT 364 414 1.
REPEAT 439 489 2.
REGION 364 489 2 X 51 AA approximate repeats.
MUTAGEN 104 104 R->H: In nusA10-1.
{ECO:0000269|PubMed:1847365}.
MUTAGEN 181 181 G->D: In nusa11; inability to terminate
transcription normally at termination
sites. {ECO:0000269|PubMed:1847365}.
MUTAGEN 183 183 L->R: In nusA1; restricts lambda growth
by preventing antitermination activity of
lambda N protein.
{ECO:0000269|PubMed:1847365}.
MUTAGEN 212 212 E->K: In nusA10-2.
{ECO:0000269|PubMed:1847365}.
CONFLICT 167 191 MLPRENFRPGDRVRGVLYSVRPEAR -> SCRVKTFALATA
FVACSIPFARNG (in Ref. 1; CAA25200).
{ECO:0000305}.
HELIX 3 16 {ECO:0000244|PDB:2KWP}.
HELIX 20 39 {ECO:0000244|PDB:2KWP}.
STRAND 45 50 {ECO:0000244|PDB:2KWP}.
TURN 51 54 {ECO:0000244|PDB:2KWP}.
STRAND 55 65 {ECO:0000244|PDB:2KWP}.
TURN 71 73 {ECO:0000244|PDB:2KWP}.
STRAND 74 76 {ECO:0000244|PDB:2KWP}.
HELIX 77 84 {ECO:0000244|PDB:2KWP}.
STRAND 92 96 {ECO:0000244|PDB:2KWP}.
HELIX 102 104 {ECO:0000244|PDB:2KWP}.
HELIX 107 123 {ECO:0000244|PDB:2KWP}.
HELIX 354 363 {ECO:0000244|PDB:1U9L}.
HELIX 367 375 {ECO:0000244|PDB:1U9L}.
HELIX 381 386 {ECO:0000244|PDB:1U9L}.
HELIX 389 392 {ECO:0000244|PDB:1U9L}.
TURN 395 397 {ECO:0000244|PDB:1WCL}.
HELIX 400 417 {ECO:0000244|PDB:1U9L}.
HELIX 432 435 {ECO:0000244|PDB:1WCN}.
HELIX 442 449 {ECO:0000244|PDB:1WCN}.
TURN 450 452 {ECO:0000244|PDB:1WCN}.
HELIX 456 460 {ECO:0000244|PDB:1WCN}.
HELIX 464 468 {ECO:0000244|PDB:1WCN}.
STRAND 470 472 {ECO:0000244|PDB:1WCN}.
HELIX 475 489 {ECO:0000244|PDB:1WCN}.
TURN 491 493 {ECO:0000244|PDB:2JZB}.
SEQUENCE 495 AA; 54871 MW; 7D4DD019172FBAD0 CRC64;
MNKEILAVVE AVSNEKALPR EKIFEALESA LATATKKKYE QEIDVRVQID RKSGDFDTFR
RWLVVDEVTQ PTKEITLEAA RYEDESLNLG DYVEDQIESV TFDRITTQTA KQVIVQKVRE
AERAMVVDQF REHEGEIITG VVKKVNRDNI SLDLGNNAEA VILREDMLPR ENFRPGDRVR
GVLYSVRPEA RGAQLFVTRS KPEMLIELFR IEVPEIGEEV IEIKAAARDP GSRAKIAVKT
NDKRIDPVGA CVGMRGARVQ AVSTELGGER IDIVLWDDNP AQFVINAMAP ADVASIVVDE
DKHTMDIAVE AGNLAQAIGR NGQNVRLASQ LSGWELNVMT VDDLQAKHQA EAHAAIDTFT
KYLDIDEDFA TVLVEEGFST LEELAYVPMK ELLEIEGLDE PTVEALRERA KNALATIAQA
QEESLGDNKP ADDLLNLEGV DRDLAFKLAA RGVCTLEDLA EQGIDDLADI EGLTDEKAGA
LIMAARNICW FGDEA


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