RegulonDB

Gene
Name:	degP
Synonym(s):	ECK0160, EG10463, b0161, htrA, ptd
Genome position(nucleotides):	180884 --> 182308
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	53.96
External database links:

ASAP:	ABE-0000551
CGSC:	30554
ECHOBASE:	EB0458
ECOLIHUB:	degP
MIM:	616779
MIM:	600142
MIM:	610149
OU-MICROARRAY:	b0161
STRING:	511145.b0161
COLOMBOS:	degP

Gene

Name:

degP

Synonym(s):

ECK0160, EG10463, b0161, htrA, ptd

Genome position(nucleotides):

180884 --> 182308

Strand:

forward

Sequence:

Get nucleotide sequence FastaFormat

GC content %:

53.96

External database links:

ASAP:

CGSC:

ECHOBASE:

ECOLIHUB:

MIM:

MIM:

MIM:

OU-MICROARRAY:

STRING:

COLOMBOS:

Type

Positions

Sequence

Comment

1 -> 26

MKKTTLALSALALSLGLALSPLSATA

10 -> 10

UniProt: In Ref. 1; AAA23994 and 7; AAA23680..

27 -> 474

AETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ

UniProt: Periplasmic serine endoprotease DegP.

46 -> 46

UniProt: In Ref. 6; AAA23717..

64 -> 105

NTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGG

DegP loop structures (LA, LD, L1, L2 and L3) are implicated in regulating protease activity

Type

Positions

Sequence

Comment

1 -> 26

MKKTTLALSALALSLGLALSPLSATA

10 -> 10

UniProt: In Ref. 1; AAA23994 and 7; AAA23680..

27 -> 474

UniProt: Periplasmic serine endoprotease DegP.

46 -> 46

UniProt: In Ref. 6; AAA23717..

64 -> 105

NTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGG

DegP loop structures (LA, LD, L1, L2 and L3) are implicated in regulating protease activity

114 -> 250

GSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGI

131 -> 131

UniProt: Loss of peptidase activity with no detectable changes in secondary structure..

192 -> 192

UniProt: In Ref. 1; AAA23994/CAA30997..

195 -> 201

NPFGLGE

DegP loop structures (LA, LD, L1, L2 and L3) are implicated in regulating protease activity

202 -> 202

T → V: weak and non-cooperative substrate binding; severely dimished substrate degradation, mutant protein can assemble into cage-like structures but component trimers remain in inactive conformation

207 -> 207

R → P: increases the equilibrium fraction of active enzyme compared with the wild type; result is dominant leethality when combined with Y444A

213 -> 213

R → A: weak and non-cooperative substrate binding; severely dimished substrate degradation, mutant protein can assemble into cage-like structures but component trimers remain in inactive conformation

226 -> 226

Q → A: weak and non-cooperative substrate binding; severely dimished substrate degradation, mutant protein can assemble into cage-like structures but component trimers remain in inactive conformation

231 -> 235

INRGN

Loop L1 of the serine protease domain

234 -> 236

GNS

UniProt: Substrate binding; Sequence Annotation Type: region of interest.

236 -> 236

UniProt: Loss of peptidase activity with no detectable changes in secondary structure..

252 -> 256

TAILA

UniProt: Substrate binding; Sequence Annotation Type: region of interest.

254 -> 264

ILAPDGGNIGI

Loop L2 of the serine protease domain

255 -> 255

UniProt: Loss of proteolytic activity..

258 -> 258

UniProt: Increases the proteolytic activity..

261 -> 261

UniProt: Loss of proteolytic activity..

262 -> 262

UniProt: Stimulates the proteolytic activity at low temperatures (20-30 degrees Celsius), whereas at higher temperatures (above 35 degrees Celsius), the proteolytic activity is less efficient..

264 -> 264

UniProt: Loss of proteolytic activity..

280 -> 371

MVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDG

UniProt: PDZ 1.

287 -> 397

KRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGI

288 -> 288

R → A: loss of allosteric activation

291 -> 291

L → W: unable to bind model peptide, does not assemble into higher order oligomers and has no protease activity in vitro

297 -> 380

ELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLEL

354 -> 354

V → S: loss of allosteric activation

377 -> 466

NLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGD

UniProt: PDZ 2.

393 -> 463

IFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQ

408 -> 469

DQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTI

467 -> 474

STIYLLMQ

UniProt: In Ref. 1; AAA23994/CAA30997..

470 -> 470

Y → A: prevents cage assembly; mutant enzyme is predominantly trimeric in the presence or absence of model substrate; supports growth at 47°C

Multifun Terms (GenProtEC)

1 - metabolism --> 1.2 - degradation of macromolecules --> 1.2.3 - proteins/peptides/glycopeptides

2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation

5 - cell processes --> 5.5 - adaptations --> 5.5.2 - temperature extremes

5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)

Gene Ontology Terms (GO)

cellular_component

GO:0016020 - membrane
GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
GO:0005886 - plasma membrane

molecular_function

GO:0005515 - protein binding
GO:0008233 - peptidase activity
GO:0016787 - hydrolase activity
GO:0004252 - serine-type endopeptidase activity
GO:0008236 - serine-type peptidase activity
GO:0042802 - identical protein binding

biological_process

GO:0006457 - protein folding
GO:0006508 - proteolysis
GO:0006515 - protein quality control for misfolded or incompletely synthesized proteins
GO:0006979 - response to oxidative stress
GO:0009266 - response to temperature stimulus
GO:0009408 - response to heat
GO:0061077 - chaperone-mediated protein folding

Transcriptional Regulation
	Display Regulation
Activated by:	CpxR
Repressed by:	H-NS

Transcriptional Regulation

Display Regulation

Activated by:

CpxR

Repressed by:

H-NS

Type	Name	Post Left	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
promoter	TSS_303 (cluster)	180836	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_304	180844	forward	nd	[RS-EPT-CBR]	[1]
promoter	TSS_305	180846	forward	nd	[RS-EPT-CBR]	[1]

Type

Name

Post Left

Post Right

Strand

Notes

Evidence (Confirmed, Strong, Weak)

References

promoter

TSS_303 (cluster)

180836

forward

[RS-EPT-CBR]

[1]

promoter

TSS_304

180844

forward

[RS-EPT-CBR]

[1]

promoter

TSS_305

180846

forward

[RS-EPT-CBR]

[1]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Evidence

[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

Reference(s)

[1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.