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DNA-binding response regulator MtrA

 MTRA_MYCTU              Reviewed;         228 AA.
P9WGM7; L0TES0; P0A5Z4; Q50447;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-OCT-2017, entry version 24.
RecName: Full=DNA-binding response regulator MtrA;
Name=mtrA; OrderedLocusNames=Rv3246c; ORFNames=MTCY20B11.21c;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION, AND INDUCTION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=8655513; DOI=10.1128/jb.178.11.3314-3321.1996;
Via L.E., Curcic R., Mudd M.H., Dhandayuthapani S., Ulmer R.J.,
Deretic V.;
"Elements of signal transduction in Mycobacterium tuberculosis: in
vitro phosphorylation and in vivo expression of the response regulator
MtrA.";
J. Bacteriol. 178:3314-3321(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[3]
INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=10851001; DOI=10.1128/JB.182.13.3832-3838.2000;
Zahrt T.C., Deretic V.;
"An essential two-component signal transduction system in
Mycobacterium tuberculosis.";
J. Bacteriol. 182:3832-3838(2000).
[4]
SUBCELLULAR LOCATION, INDUCTION, DNA-BINDING, PHOSPHORYLATION AT
ASP-56, AND MUTAGENESIS OF ASP-56.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16629667; DOI=10.1111/j.1365-2958.2006.05137.x;
Fol M., Chauhan A., Nair N.K., Maloney E., Moomey M., Jagannath C.,
Madiraju M.V., Rajagopalan M.;
"Modulation of Mycobacterium tuberculosis proliferation by MtrA, an
essential two-component response regulator.";
Mol. Microbiol. 60:643-657(2006).
[5]
DNA-BINDING, AND COFACTOR.
PubMed=20671191; DOI=10.1093/jb/mvq082;
Li Y., Zeng J., He Z.G.;
"Characterization of a functional C-terminus of the Mycobacterium
tuberculosis MtrA responsible for both DNA binding and interaction
with its two-component partner protein, MtrB.";
J. Biochem. 148:549-556(2010).
[6]
FUNCTION, DNA-BINDING, PHOSPHORYLATION AT ASP-56, AND MUTAGENESIS OF
ASP-56.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20223818; DOI=10.1074/jbc.M109.040097;
Rajagopalan M., Dziedzic R., Al Zayer M., Stankowska D., Ouimet M.C.,
Bastedo D.P., Marczynski G.T., Madiraju M.V.;
"Mycobacterium tuberculosis origin of replication and the promoter for
immunodominant secreted antigen 85B are the targets of MtrA, the
essential response regulator.";
J. Biol. Chem. 285:15816-15827(2010).
[7]
PROTEASOME SUBSTRATE, PUPYLATION AT LYS-207, AND IDENTIFICATION BY
MASS SPECTROMETRY.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20066036; DOI=10.1371/journal.pone.0008589;
Festa R.A., McAllister F., Pearce M.J., Mintseris J., Burns K.E.,
Gygi S.P., Darwin K.H.;
"Prokayrotic ubiquitin-like protein (Pup) proteome of Mycobacterium
tuberculosis.";
PLoS ONE 5:E8589-E8589(2010).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[9]
FUNCTION, SUBUNIT, INTERACTION WITH MTRB, DNA-BINDING, AND MUTAGENESIS
OF ASP-13 AND ASP-56.
STRAIN=ATCC 25618 / H37Rv;
PubMed=21295603; DOI=10.1016/j.plasmid.2011.01.002;
Al Zayer M., Stankowska D., Dziedzic R., Sarva K., Madiraju M.V.,
Rajagopalan M.;
"Mycobacterium tuberculosis mtrA merodiploid strains with point
mutations in the signal-receiving domain of MtrA exhibit growth
defects in nutrient broth.";
Plasmid 65:210-218(2011).
[10]
FUNCTION, DNA-BINDING, AND MUTAGENESIS OF TYR-102.
STRAIN=ATCC 25618 / H37Rv;
PubMed=22610443; DOI=10.1074/jbc.M112.346544;
Plocinska R., Purushotham G., Sarva K., Vadrevu I.S., Pandeeti E.V.,
Arora N., Plocinski P., Madiraju M.V., Rajagopalan M.;
"Septal localization of the Mycobacterium tuberculosis MtrB sensor
kinase promotes MtrA regulon expression.";
J. Biol. Chem. 287:23887-23899(2012).
[11]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN THE INACTIVE STATE, COFACTOR,
AND PHOSPHORYLATION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=17511470; DOI=10.1021/bi602546q;
Friedland N., Mack T.R., Yu M., Hung L.W., Terwilliger T.C.,
Waldo G.S., Stock A.M.;
"Domain orientation in the inactive response regulator Mycobacterium
tuberculosis MtrA provides a barrier to activation.";
Biochemistry 46:6733-6743(2007).
[12]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-125, COFACTOR, AND SUBUNIT.
STRAIN=ATCC 25618 / H37Rv;
PubMed=20702407; DOI=10.1074/jbc.M110.157164;
Barbieri C.M., Mack T.R., Robinson V.L., Miller M.T., Stock A.M.;
"Regulation of response regulator autophosphorylation through
interdomain contacts.";
J. Biol. Chem. 285:32325-32335(2010).
-!- FUNCTION: Member of the two-component regulatory system MtrA/MtrB.
Binds direct repeat motifs of sequence 5'-GTCACAGCG-3',
phosphorylation confers higher affinity. Overexpression decreases
bacteria viability upon infection of human THP-1 macrophage cell
line, due at least in part to impaired blockage of phagosome-
lysosome fusion (upon infection bacteria usually remain in
phagosomes). Infecting C57BL/6 mice with an overexpressing strain
leads to an attentuated infection in both spleen and lungs. The
level of dnaA mRNA increases dramatically. Binds the promoter of
dnaA, fbpD, ripA and itself, as well as oriC, which it may
regulate. Upon co-overexpression of MrtA and MtrB growth in
macrophages is partially restored, dnaA expression is not induced,
although mouse infections are still attenuated, suggesting that
bacterial growth in macrophages requires an optimal ratio of MtrB
to MtrA. {ECO:0000269|PubMed:20223818,
ECO:0000269|PubMed:21295603, ECO:0000269|PubMed:22610443}.
-!- COFACTOR:
Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
Evidence={ECO:0000269|PubMed:17511470,
ECO:0000269|PubMed:20671191, ECO:0000269|PubMed:20702407};
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:17511470,
ECO:0000269|PubMed:20671191, ECO:0000269|PubMed:20702407};
Note=Divalent cation. Ca(2+) and Mg(2+) have both been seen in
crystal structures. Optimal DNA-binding requires Ca(2+).
{ECO:0000269|PubMed:17511470, ECO:0000269|PubMed:20671191,
ECO:0000269|PubMed:20702407};
-!- SUBUNIT: Probably a monomer when inactive, phosphorylation may
permit it to oligomerize. It can oligomerize, and interacts with
MrtB. {ECO:0000269|PubMed:20702407, ECO:0000269|PubMed:21295603}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:16629667}.
-!- INDUCTION: Expressed in culture (at protein level). Constitutively
expressed in infected human blood-derived macrophages and mouse
macrophage cell line J774A. Autoregulates its own expression.
{ECO:0000269|PubMed:10851001, ECO:0000269|PubMed:16629667,
ECO:0000269|PubMed:8655513}.
-!- DOMAIN: C-terminal domain binds DNA and interacts with MtrB.
-!- PTM: Phosphorylated by MtrB (Probable). Autophosphorylates very
slowly. Phosphorylated protein binds DNA better than
unphosphorylated. {ECO:0000269|PubMed:16629667,
ECO:0000269|PubMed:17511470, ECO:0000269|PubMed:20223818,
ECO:0000305}.
-!- PTM: Pupylated at Lys-207 by the prokaryotic ubiquitin-like
protein Pup, which leads to its degradation by the proteasome.
{ECO:0000269|PubMed:20066036}.
-!- DISRUPTION PHENOTYPE: Essential, it cannot be disrupted.
{ECO:0000269|PubMed:10851001}.
-!- MISCELLANEOUS: Was identified as a natural substrate of the
M.tuberculosis proteasome.
-!- SEQUENCE CAUTION:
Sequence=AAB07804.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U01971; AAB07804.1; ALT_INIT; Genomic_DNA.
EMBL; AL123456; CCP46065.1; -; Genomic_DNA.
PIR; H70592; H70592.
RefSeq; NP_217763.1; NC_000962.3.
RefSeq; WP_003899985.1; NZ_KK339370.1.
PDB; 2GWR; X-ray; 2.10 A; A=1-228.
PDB; 3NHZ; X-ray; 2.50 A; A/B/C/D=1-125.
PDBsum; 2GWR; -.
PDBsum; 3NHZ; -.
ProteinModelPortal; P9WGM7; -.
SMR; P9WGM7; -.
STRING; 83332.Rv3246c; -.
PaxDb; P9WGM7; -.
EnsemblBacteria; CCP46065; CCP46065; Rv3246c.
GeneID; 888743; -.
KEGG; mtu:Rv3246c; -.
TubercuList; Rv3246c; -.
eggNOG; ENOG4105CK6; Bacteria.
eggNOG; COG0745; LUCA.
KO; K07670; -.
PhylomeDB; P9WGM7; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0044117; P:growth of symbiont in host; IMP:MTBBASE.
GO; GO:0000160; P:phosphorelay signal transduction system; IEA:UniProtKB-KW.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:MTBBASE.
GO; GO:0006468; P:protein phosphorylation; IDA:MTBBASE.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
CDD; cd00156; REC; 1.
CDD; cd00383; trans_reg_C; 1.
Gene3D; 1.10.10.10; -; 1.
InterPro; IPR011006; CheY-like_superfamily.
InterPro; IPR001867; OmpR/PhoB-type_DNA-bd.
InterPro; IPR001789; Sig_transdc_resp-reg_receiver.
InterPro; IPR036388; WH-like_DNA-bd_sf.
Pfam; PF00072; Response_reg; 1.
Pfam; PF00486; Trans_reg_C; 1.
SMART; SM00448; REC; 1.
SMART; SM00862; Trans_reg_C; 1.
SUPFAM; SSF52172; SSF52172; 1.
PROSITE; PS51755; OMPR_PHOB; 1.
PROSITE; PS50110; RESPONSE_REGULATORY; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; DNA-binding;
Isopeptide bond; Metal-binding; Phosphoprotein; Reference proteome;
Transcription; Transcription regulation;
Two-component regulatory system; Ubl conjugation.
CHAIN 1 228 DNA-binding response regulator MtrA.
/FTId=PRO_0000081143.
DOMAIN 7 120 Response regulatory.
{ECO:0000255|PROSITE-ProRule:PRU00169}.
DNA_BIND 128 227 OmpR/PhoB-type. {ECO:0000255|PROSITE-
ProRule:PRU01091}.
METAL 13 13 Divalent metal cation.
METAL 56 56 Divalent metal cation.
METAL 59 59 Divalent metal cation; via carbonyl
oxygen.
MOD_RES 56 56 4-aspartylphosphate.
{ECO:0000255|PROSITE-ProRule:PRU00169,
ECO:0000269|PubMed:16629667,
ECO:0000269|PubMed:20223818}.
CROSSLNK 207 207 Isoglutamyl lysine isopeptide (Lys-Gln)
(interchain with Q-Cter in protein Pup).
{ECO:0000269|PubMed:20066036}.
MUTAGEN 13 13 D->A: No phosphorylation by EnvZ kinase
in vitro. Binds fbpB and oriC DNA in the
presence and absence of EnvZ and ATP. A
merodiploid strain has late growth
defects, fbpB is down-regulated. May be
constitutively active.
{ECO:0000269|PubMed:21295603}.
MUTAGEN 56 56 D->E: No phosphorylation by EnvZ kinase
in vitro. Binds DNA in the absence but
not presence of EnvZ and ATP. A
merodiploid strain has late growth
defects. May mimic the phosphorylated
state. {ECO:0000269|PubMed:16629667,
ECO:0000269|PubMed:20223818,
ECO:0000269|PubMed:21295603}.
MUTAGEN 56 56 D->N: No phosphorylation by EnvZ kinase
in vitro, does not bind DNA. Poor growth
in infected macrophages and upon mouse
infection. Fewer bacteria are mistargeted
to lysosomes.
{ECO:0000269|PubMed:16629667,
ECO:0000269|PubMed:20223818,
ECO:0000269|PubMed:21295603}.
MUTAGEN 102 102 Y->C: Phosphorylated by EnvZ kinase in
vitro, reverses many phenotypes of mtrB
knockout. {ECO:0000269|PubMed:22610443}.
STRAND 7 11 {ECO:0000244|PDB:2GWR}.
HELIX 15 27 {ECO:0000244|PDB:2GWR}.
STRAND 31 35 {ECO:0000244|PDB:2GWR}.
HELIX 38 40 {ECO:0000244|PDB:2GWR}.
HELIX 41 48 {ECO:0000244|PDB:2GWR}.
STRAND 51 58 {ECO:0000244|PDB:2GWR}.
STRAND 60 62 {ECO:0000244|PDB:2GWR}.
HELIX 64 72 {ECO:0000244|PDB:2GWR}.
STRAND 79 84 {ECO:0000244|PDB:2GWR}.
HELIX 91 96 {ECO:0000244|PDB:2GWR}.
STRAND 101 106 {ECO:0000244|PDB:2GWR}.
HELIX 109 119 {ECO:0000244|PDB:2GWR}.
STRAND 130 133 {ECO:0000244|PDB:2GWR}.
STRAND 136 139 {ECO:0000244|PDB:2GWR}.
TURN 140 143 {ECO:0000244|PDB:2GWR}.
STRAND 144 147 {ECO:0000244|PDB:2GWR}.
STRAND 150 152 {ECO:0000244|PDB:2GWR}.
HELIX 156 167 {ECO:0000244|PDB:2GWR}.
HELIX 175 181 {ECO:0000244|PDB:2GWR}.
HELIX 192 205 {ECO:0000244|PDB:2GWR}.
STRAND 213 218 {ECO:0000244|PDB:2GWR}.
TURN 219 221 {ECO:0000244|PDB:2GWR}.
STRAND 222 225 {ECO:0000244|PDB:2GWR}.
SEQUENCE 228 AA; 25279 MW; 925DEBC495DFD5B6 CRC64;
MDTMRQRILV VDDDASLAEM LTIVLRGEGF DTAVIGDGTQ ALTAVRELRP DLVLLDLMLP
GMNGIDVCRV LRADSGVPIV MLTAKTDTVD VVLGLESGAD DYIMKPFKPK ELVARVRARL
RRNDDEPAEM LSIADVEIDV PAHKVTRNGE QISLTPLEFD LLVALARKPR QVFTRDVLLE
QVWGYRHPAD TRLVNVHVQR LRAKVEKDPE NPTVVLTVRG VGYKAGPP


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