P14147 (PHOQ_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Virulence sensor histidine kinase PhoQ
EC=2.7.13.3

Gene names

Name:	phoQ
Ordered Locus Names:	STM1230

Organism

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]

Taxonomic identifier

99287 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella › Salmonella choleraesuis › Salmonella enterica I › Salmonella typhimurium

Protein attributes

Sequence length	487 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Member of the two-component regulatory system PhoQ/PhoP which regulates the expression of genes involved in virulence, adaptation to low Mg2+ environments and resistance to host defense antimicrobial peptides. In presence of low periplasmic Mg2+ concentrations, PhoQ functions as a membrane-associated protein kinase that undergoes autophosphorylation and subsequently transfers the phosphate to PhoP, which results in the expression of PhoP-activated genes (PAG) and repression of PhoP-repressed genes (PRG). In presence of high periplasmic Mg2+ concentrations, acts as a protein phosphatase that dephosphorylates phospho-PhoP, which results in the repression of PhoP-activated genes and may lead to expression of some PhoP-repressed genes. Promotes intramacrophage survival of S.typhimurium. Is essential for transcription of spiC inside macrophages by controlling the expression of the two-component regulatory system ssrB/ssrA and pir at transcriptional and post-transcriptional levels respectively. Promotes expression of the two-component regulatory system pmrA/pmrB via activation of pmrD gene. Is required to attenuate bacterial growth within fibroblast cells and to enhance bacterial resistance to bile in intestinal cells. Also, negatively regulates prgH, which is required for invasion of epithelial cells. Ref.5 Ref.8 Ref.9 Ref.14 Ref.16 Ref.17
Catalytic activity	ATP + protein L-histidine = ADP + protein N-phospho-L-histidine. Ref.11 Ref.12
Enzyme regulation	Autokinase and kinase activities depend on low (micromolar range) Mg2+ concentrations. Phosphatase activity is stimulated by high (millimolar range) Mg2+ concentrations and ADP at 1 mM. Ref.10 Ref.16
Subunit structure	Homodimer By similarity.
Subcellular location	Cell inner membrane; Multi-pass membrane protein By similarity.
Induction	The phoQ/phoP operon is positively autoregulated by both PhoP and PhoQ in a Mg2+-dependent manner. Repressed by RcsB via sigma factor RpoS. Ref.6 Ref.7 Ref.10 Ref.14 Ref.15 Ref.16
Miscellaneous	Substitutions experiments show that amino acid Thr-48 may be involved in the conformational changes responsible for the balance between kinase-dominant state and phosphatase-dominant state. The PhoQ/PhoP-signaling cascade, which activates virulence membrane genes (pagC, pagO, pagD, pagK, pgtE and phoN), is induced by cationic antimicrobial peptides (CAMP) (polymyxin, alpha-helical peptide C18G and sheet peptide protegrin-1) at sublethal concentrations.
Sequence similarities	Contains 1 HAMP domain. Contains 1 histidine kinase domain.

Ontologies

Keywords
Biological process	Growth regulation Two-component regulatory system Virulence
Cellular component	Cell inner membrane Cell membrane Membrane
Domain	Transmembrane Transmembrane helix
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	pathogenesis Inferred from electronic annotation. Source: UniProtKB-KW peptidyl-histidine phosphorylation Inferred from electronic annotation. Source: InterPro regulation of growth Inferred from electronic annotation. Source: UniProtKB-KW signal transduction by phosphorylation Inferred from electronic annotation. Source: GOC
Cellular_component	integral to membrane Inferred from electronic annotation. Source: UniProtKB-KW plasma membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorelay sensor kinase activity 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 – 487

487

Virulence sensor histidine kinase PhoQ

PRO_0000074843

Regions

Topological domain

1 – 16

16

Cytoplasmic Potential

Transmembrane

17 – 37

21

Helical; Potential

Topological domain

38 – 193

156

Periplasmic Potential

Transmembrane

194 – 214

21

Helical; Potential

Topological domain

215 – 487

273

Cytoplasmic Potential

Domain

215 – 266

52

HAMP

Domain

274 – 481

208

Histidine kinase

Nucleotide binding

386 – 394

9

ATP By similarity

Nucleotide binding

416 – 421

6

ATP By similarity

Nucleotide binding

435 – 447

13

ATP By similarity

Sites

Metal binding

151

1

Divalent metal cation By similarity

Metal binding

152

1

Divalent metal cation By similarity

Metal binding

386

1

Magnesium By similarity

Metal binding

443

1

Magnesium By similarity

Site

202

1

Plays a critical role in the switching between kinase and phosphatase states By similarity

Amino acid modifications

Modified residue

277

1

Phosphohistidine; by autocatalysis

Natural variations

Natural variant

82 – 99

18

Missing in strain: ATCC 10428.

Natural variant

442 – 459

18

Missing in strain: ATCC 10428.

Experimental info

Mutagenesis

47

1

T → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

48

1

T → A: Confers to cells a PhoP wild-type phenotype. No effect on net phosphorylation of PhoP. Decreases 5-fold initial rate of autophosphorylation and increases phosphatase activity. Ref.4 Ref.12

Mutagenesis

48

1

T → I: Low affinity for Ca(2+). Confers to cells a PhoP constitutively active phenotype. Affects PhoQ/PhoP-signaling cascade and increase net phosphorylation of PhoP. No effect on initial rate of autophosphorylation and decreases phosphatase activity. Ref.4 Ref.12

Mutagenesis

48

1

T → L: Confers to cells a PhoP constitutively inactive phenotype. Affects PhoQ/PhoP-signaling cascade but no significantly effect on net phosphorylation of PhoP. Decreases 3-fold initial rate of autophosphorylation and increases phosphatase activity. Ref.4 Ref.12

Mutagenesis

48

1

T → S: Confers to cells a PhoP wild-type phenotype. No effect on net phosphorylation of PhoP. Decreases 5-fold initial rate of autophosphorylation and shows a wild-type phosphatase activity. Ref.4 Ref.12

Mutagenesis

48

1

T → V: Confers to cells a PhoP constitutively active phenotype. Affects PhoQ/PhoP-signaling cascade and increases net phosphorylation of PhoP. No effect on initial rate of autophosphorylation and decreases phosphatase activity. Ref.4 Ref.12

Mutagenesis

83

1

P → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

88

1

I → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

89

1

Y → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

93

1

G → A: Retains a wild-type Mg(2+) response. Less sensitive to Mg(2+) response than wild-type and defective in Mg(2+) binding; when associated with R-97. Ref.13

Mutagenesis

96

1

L → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

97

1

W → A: Retains a wild-type Mg(2+) response. Ref.13

Mutagenesis

97

1

W → R: Less sensitive to Mg(2+) response than wild-type and defective in Mg(2+) binding; when associated with A-93. Ref.13

Mutagenesis

120

1

H → A: Less sensitive to Mg(2+)response and defective in Mg(2+) binding than wild-type. Ref.13

Mutagenesis

149

1

D → A: Less sensitive to Mg(2+) response than wild-type. Retains a wild-type Mg(2+) response in strain PhoP* PhoQ expressing mutant phoP N-93. Ref.13

Mutagenesis

150

1

D → A: Less sensitive to Mg(2+) response than wild-type in strain PhoP* PhoQ expressing mutant phoP N-93. Ref.13

Mutagenesis

151

1

D → A: Less sensitive to Mg(2+) response than wild-type in strain PhoP* PhoQ expressing mutant phoP N-93. Ref.13

Mutagenesis

152

1

D → A: Less sensitive to Mg(2+) response than wild-type in strain PhoP* PhoQ expressing mutant phoP N-93. Ref.13

Mutagenesis

156

1

T → A: Less sensitive to Mg(2+) response and defective binding than wild-type. Ref.13

Mutagenesis

277

1

H → A: Retains a wild-type Mg(2+) response only at 10 mM. Ref.10 Ref.11 Ref.13

Mutagenesis

277

1

H → N: Abolishes autophosphorylation activity. Ref.10 Ref.11 Ref.13

Mutagenesis

277

1

H → V: Retains a wild-type Mg(2+) response only at 10 mM in strain PhoP* PhoQ expressing mutant phoP N-93. Loss of autophosphorylation, irrespective of the presence of Mg(2+). Unable to promote phoP dephosphorylation even in presence of added Mg(2+). Ref.10 Ref.11 Ref.13

Mutagenesis

313

1

R → W: Increased ability to proliferate within fibroblasts. Ref.2

Secondary structure

1

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487

Helix Strand Turn

Details...

Helix

46 – 62

17

Beta strand

63 – 65

3

Beta strand

70 – 72

3

Beta strand

83 – 89

7

Beta strand

95 – 100

6

Helix

103 – 108

6

Helix

111 – 115

5

Beta strand

116 – 125

10

Helix

126 – 132

7

Helix

139 – 149

11

Beta strand

154 – 164

11

Beta strand

173 – 181

9

Helix

183 – 185

3

Beta strand

333 – 335

3

Beta strand

338 – 340

3

Helix

341 – 355

15

Turn

356 – 360

5

Beta strand

362 – 366

5

Beta strand

372 – 375

4

Helix

377 – 394

18

Beta strand

396 – 406

11

Beta strand

409 – 418

10

Helix

445 – 447

3

Helix

448 – 456

9

Beta strand

460 – 465

6

Beta strand

469 – 477

9

Beta strand

482 – 485

4

Sequences

	Sequence		Length	Mass (Da)
	P14147 [UniParc]. Last modified January 23, 2002. Version 2. Checksum: BDCFEFC56F4CA058	FASTA	487	55,467
	10 20 30 40 50 60 MNKFARHFLP LSLRVRFLLA TAGVVLVLSL AYGIVALVGY SVSFDKTTFR LLRGESNLFY 70 80 90 100 110 120 TLAKWENNKI SVELPENLDM QSPTMTLIYD ETGKLLWTQR NIPWLIKSIQ PEWLKTNGFH 130 140 150 160 170 180 EIETNVDATS TLLSEDHSAQ EKLKEVREDD DDAEMTHSVA VNIYPATARM PQLTIVVVDT 190 200 210 220 230 240 IPIELKRSYM VWSWFVYVLA ANLLLVIPLL WIAAWWSLRP IEALAREVRE LEDHHREMLN 250 260 270 280 290 300 PETTRELTSL VRNLNQLLKS ERERYNKYRT TLTDLTHSLK TPLAVLQSTL RSLRNEKMSV 310 320 330 340 350 360 SKAEPVMLEQ ISRISQQIGY YLHRASMRGS GVLLSRELHP VAPLLDNLIS ALNKVYQRKG 370 380 390 400 410 420 VNISMDISPE ISFVGEQNDF VEVMGNVLDN ACKYCLEFVE ISARQTDDHL HIFVEDDGPG 430 440 450 460 470 480 IPHSKRSLVF DRGQRADTLR PGQGVGLAVA REITEQYAGQ IIASDSLLGG ARMEVVFGRQ HPTQKEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A two-component regulatory system (phoP phoQ) controls Salmonella typhimurium virulence." Miller S.I., Kukral A.M., Mekalanos J.J. Proc. Natl. Acad. Sci. U.S.A. 86:5054-5058(1989) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 14028 / SGSG 2980 / CDC 6516-60 / NCTC 12023.
[2]	"Salmonella enterica serovar Typhimurium response involved in attenuation of pathogen intracellular proliferation." Cano D.A., Martinez-Moya M., Pucciarelli M.G., Groisman E.A., Casadesus J., Garcia-del Portillo F. Infect. Immun. 69:6463-6474(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF ARG-313. Strain: SL1344.
[3]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.
[4]	"Characterization of the bacterial sensor protein PhoQ. Evidence for distinct binding sites for Mg2+ and Ca2+." Garcia Vescovi E., Ayala Y.M., Di Cera E., Groisman E.A. J. Biol. Chem. 272:1440-1443(1997) [PubMed] [Europe PMC] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, DIVALENT CATIONS-BINDING SITES, MUTAGENESIS OF THR-48. Strain: ATCC 14028s / SGSG 2262.
[5]	"A PhoP-repressed gene promotes Salmonella typhimurium invasion of epithelial cells." Behlau I., Miller S.I. J. Bacteriol. 175:4475-4484(1993) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: ATCC 14028s / SGSG 2262.
[6]	"Transcriptional autoregulation of the Salmonella typhimurium phoPQ operon." Soncini F.C., Garcia Vescovi E., Groisman E.A. J. Bacteriol. 177:4364-4371(1995) [PubMed] [Europe PMC] [Abstract] Cited for: AUTOREGULATION. Strain: ATCC 14028s / SGSG 2262.
[7]	"Mg2+ as an extracellular signal: environmental regulation of Salmonella virulence." Garcia Vescovi E., Soncini F.C., Groisman E.A. Cell 84:165-174(1996) [PubMed] [Europe PMC] [Abstract] Cited for: REGULATION BY MG(2+). Strain: ATCC 14028s / SGSG 2262.
[8]	"PhoP-PhoQ-regulated loci are required for enhanced bile resistance in Salmonella spp." van Velkinburgh J.C., Gunn J.S. Infect. Immun. 67:1614-1622(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: ATCC 14028s / SGSG 2262.
[9]	"A small protein that mediates the activation of a two-component system by another two-component system." Kox L.F.F., Woesten M.M.S.M., Groisman E.A. EMBO J. 19:1861-1872(2000) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: ATCC 14028s / SGSG 2262.
[10]	"The phosphatase activity is the target for Mg2+ regulation of the sensor protein PhoQ in Salmonella." Castelli M.E., Garcia Vescovi E., Soncini F.C. J. Biol. Chem. 275:22948-22954(2000) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHATASE ACTIVITY, ENZYME REGULATION, MUTAGENESIS OF HIS-277.
[11]	"Characterization of the catalytic activities of the PhoQ histidine protein kinase of Salmonella enterica serovar Typhimurium." Montagne M., Martel A., Le Moual H. J. Bacteriol. 183:1787-1791(2001) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, MUTAGENESIS OF HIS-277.
[12]	"Mutational analysis of the residue at position 48 in the Salmonella enterica Serovar Typhimurium PhoQ sensor kinase." Sanowar S., Martel A., Le Moual H. J. Bacteriol. 185:1935-1941(2003) [PubMed] [Europe PMC] [Abstract] Cited for: CATALYTIC ACTIVITY, MUTAGENESIS OF THR-48.
[13]	"Mg2+ sensing by the Mg2+ sensor PhoQ of Salmonella enterica." Chamnongpol S., Cromie M., Groisman E.A. J. Mol. Biol. 325:795-807(2003) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF THR-47; PRO-83; ILE-88; TYR-89; GLY-93; LEU-96; TRP-97; HIS-120; ASP-149; ASP-150; ASP-151; ASP-152; THR-156 AND HIS-277. Strain: ATCC 14028s / SGSG 2262.
[14]	"Regulation of Salmonella typhimurium virulence gene expression by cationic antimicrobial peptides." Bader M.W., Navarre W.W., Shiau W., Nikaido H., Frye J.G., McClelland M., Fang F.C., Miller S.I. Mol. Microbiol. 50:219-230(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, REGULATION BY CATIONIC ANTIMICROBIAL PEPTIDES (CAMP). Strain: ATCC 14028s / SGSG 2262.
[15]	"The Salmonella membrane protein IgaA modulates the activity of the RcsC-YojN-RcsB and PhoP-PhoQ regulons." Tierrez A., Garcia-del Portillo F. J. Bacteriol. 186:7481-7489(2004) [PubMed] [Europe PMC] [Abstract] Cited for: REGULATION BY RCSB. Strain: SL1344.
[16]	"Functional reconstitution of the Salmonella typhimurium PhoQ histidine kinase sensor in proteoliposomes." Sanowar S., Le Moual H. Biochem. J. 390:769-776(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, ENZYME REGULATION.
[17]	"The PhoP/PhoQ system controls the intramacrophage type three secretion system of Salmonella enterica." Bijlsma J.J.E., Groisman E.A. Mol. Microbiol. 57:85-96(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION. Strain: ATCC 14028s / SGSG 2262.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M24424 Genomic DNA. Translation: AAA27189.1.
AJ272210 Genomic DNA. Translation: CAB75592.1.
AE006468 Genomic DNA. Translation: AAL20159.1.

PIR

VZEBPT. B32932.

RefSeq

NP_460200.1. NC_003197.1.
YP_005181080.1. NC_016810.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1YAX	X-ray	2.40	A/B/C/D	45-190	[»]
3CGY	X-ray	2.60	A/B/C	332-487	[»]
3CGZ	X-ray	1.90	A/B/C	332-487	[»]

ProteinModelPortal

P14147.

SMR

P14147. Positions 45-190, 332-487.

ModBase

Search...

Protein-protein interaction databases

STRING

99287.STM1230.

Proteomic databases

PRIDE

P14147.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAL20159; AAL20159; STM1230.

GeneID

11764645.
1252748.

KEGG

sey:SL1344_1168.
stm:STM1230.

PATRIC

32380913. VBISalEnt20916_1301.

Phylogenomic databases

HOGENOM

HOG000274481.

KO

K07637.

OMA

AHWSLRP.

ProtClustDB

PRK10815.

Enzyme and pathway databases

BRENDA

2.7.13.3. 5542.

Family and domain databases

Gene3D

3.30.565.10. 1 hit.

InterPro

IPR003660. HAMP_linker_domain.
IPR003594. HATPase_ATP-bd.
IPR015014. PhoQ_Sensor.
IPR004358. Sig_transdc_His_kin-like_C.
IPR003661. Sig_transdc_His_kin_sub1_dim/P.
IPR005467. Sig_transdc_His_kinase_core.
[Graphical view]

Pfam

PF00672. HAMP. 1 hit.
PF02518. HATPase_c. 1 hit.
PF08918. PhoQ_Sensor. 1 hit.
[Graphical view]

PRINTS

PR00344. BCTRLSENSOR.

SMART

SM00387. HATPase_c. 1 hit.
SM00388. HisKA. 1 hit.
[Graphical view]

SUPFAM

SSF55874. ATP_bd_ATPase. 1 hit.

PROSITE

PS50885. HAMP. 1 hit.
PS50109. HIS_KIN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChEMBL

CHEMBL6096.

EvolutionaryTrace

P14147.

Entry information

Entry name

PHOQ_SALTY

Accession

Primary (citable) accession number: P14147
Secondary accession number(s): Q9L3L1

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 1, 1990
Last sequence update:	January 23, 2002
Last modified:	May 1, 2013
This is version 131 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program