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Protein

Serine endoprotease DegS

Gene

degS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

A site-1 protease (S1P) that cleaves the peptide bond between 'Val-148' and 'Ser-149' in RseA. Part of a regulated intramembrane proteolysis (RIP) cascade. When heat shock or other environmental stresses disrupt protein folding in the periplasm, DegS senses the accumulation of unassembled outer membrane porins (OMP) and then initiates RseA (anti sigma-E factor) degradation by cleaving its periplasmic domain, making it a substrate for subsequent cleavage by RseP. This cascade ultimately leads to the sigma-E-driven expression of a variety of factors dealing with folding stress in the periplasm and OMP assembly. Required for basal and stress-induced degradation of RseA.10 Publications

Catalytic activityi

Acts on substrates that are at least partially unfolded. The cleavage site P1 residue is normally between a pair of hydrophobic residues, such as Val-|-Val.

Enzyme regulationi

Allosterically activated by the C-terminus of exposed OMP peptides (consensus Tyr-X-Phe-COOH); cleavage only occurs in the presence of peptides. Inhibited when RseB is bound to RseA.5 Publications

Kineticsi

  1. KM=33 µM for RseA-YQF2 Publications
  1. Vmax=0.6 µmol/sec/mg enzyme2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Active sitei96Charge relay system3 Publications1
Active sitei126Charge relay system3 Publications1
Binding sitei184Substrate1
Active sitei201Charge relay system3 Publications1
Binding sitei351Substrate1

GO - Molecular functioni

  • peptidase activity Source: EcoliWiki
  • serine-type endopeptidase activity Source: EcoCyc
  • serine-type peptidase activity Source: EcoliWiki

GO - Biological processi

  • cellular response to misfolded protein Source: EcoCyc
  • proteolysis Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase, Protease, Serine protease

Enzyme and pathway databases

BioCyciEcoCyc:EG11652-MONOMER.
ECOL316407:JW3204-MONOMER.
MetaCyc:EG11652-MONOMER.

Protein family/group databases

MEROPSiS01.275.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine endoprotease DegS (EC:3.4.21.107)
Alternative name(s):
Site-1 protease DegS
Short name:
S1P protease DegS
Site-1-type intramembrane protease
Gene namesi
Name:degS
Synonyms:hhoB, htrH
Ordered Locus Names:b3235, JW3204
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11652. degS.

Subcellular locationi

  • Cell inner membrane 1 Publication; Single-pass membrane protein 1 Publication

  • Note: It is unclear how this protein is anchored to the inner membrane, programs predict a signal sequence, but replacing the N-terminal 26 residues with a known signal sequence gives a protein unable to fully complement a disruption mutant.1 Publication

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 4Cytoplasmic1 Publication4
Transmembranei5 – 27HelicalSequence analysisAdd BLAST23
Topological domaini28 – 355Periplasmic1 PublicationAdd BLAST328

GO - Cellular componenti

  • integral component of external side of plasma membrane Source: EcoliWiki
  • outer membrane-bounded periplasmic space Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cell inner membrane, Cell membrane, Membrane

Pathology & Biotechi

Disruption phenotypei

Small, slowly growing colonies. 5-fold decrease in basal sigma-E (RpoE) activity, loss of regular growth regulation of sigma-E. No proteolysis of full-length RseA.5 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi122D → A: Causes substantial reduction of peptidase activity. Binds activator peptides. 2 Publications1
Mutagenesisi162Y → A: Loss of peptidase activity. Binds activator peptides. 4 Publications1
Mutagenesisi162Y → F: Loss of 60% of peptidase activity. 4 Publications1
Mutagenesisi178R → A: Causes substantial reduction of peptidase activity. 2 Publications1
Mutagenesisi183P → A: Loss of peptidase activity. Also affects an interface contact between the PDZ and protease domains. 2 Publications1
Mutagenesisi191Q → A: Loss of peptidase activity. 1 Publication1
Mutagenesisi198H → A: Behaves like wild-type. 3 Publications1
Mutagenesisi198H → P: Partially bypasses the requirement for peptide activation, acts synergistically with mutations that disrupt contacts between the protease and PDZ domains and with an rseB disruption. 3 Publications1
Mutagenesisi201S → A: Does not restore RseA degradation in a degS disruption. Loss of RseA degradation. 1 Publication1
Mutagenesisi227E → A: Loss of peptidase activity. 2 Publications1
Mutagenesisi243K → D: Increases the basal rate of RseA cleavage 3-fold, acts synergistically with an rseB disruption. 2 Publications1
Mutagenesisi256R → A: Dramatically increases the basal rate of RseA cleavage. 1 Publication1
Mutagenesisi256R → D: Dramatically increases the basal rate of RseA cleavage. 1 Publication1
Mutagenesisi320D → A: Dramatically increases the basal rate of RseA cleavage. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000269381 – 355Serine endoprotease DegSAdd BLAST355

Proteomic databases

PaxDbiP0AEE3.
PRIDEiP0AEE3.

Interactioni

Subunit structurei

Homotrimer.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
rseAP0AFX74EBI-1132101,EBI-1117560

Protein-protein interaction databases

DIPiDIP-39580N.
IntActiP0AEE3. 3 interactors.
STRINGi511145.b3235.

Structurei

Secondary structure

1355
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi39 – 41Combined sources3
Helixi48 – 54Combined sources7
Helixi55 – 57Combined sources3
Beta strandi58 – 64Combined sources7
Turni67 – 69Combined sources3
Beta strandi76 – 86Combined sources11
Turni87 – 89Combined sources3
Beta strandi90 – 94Combined sources5
Helixi95 – 98Combined sources4
Beta strandi102 – 107Combined sources6
Beta strandi113 – 122Combined sources10
Turni123 – 126Combined sources4
Beta strandi127 – 131Combined sources5
Beta strandi153 – 159Combined sources7
Helixi161 – 163Combined sources3
Beta strandi166 – 176Combined sources11
Beta strandi180 – 182Combined sources3
Beta strandi183 – 185Combined sources3
Helixi186 – 188Combined sources3
Beta strandi190 – 192Combined sources3
Turni198 – 202Combined sources5
Beta strandi204 – 206Combined sources3
Beta strandi212 – 216Combined sources5
Beta strandi220 – 225Combined sources6
Beta strandi233 – 237Combined sources5
Helixi238 – 251Combined sources14
Beta strandi261 – 265Combined sources5
Beta strandi271 – 274Combined sources4
Beta strandi276 – 278Combined sources3
Beta strandi282 – 287Combined sources6
Beta strandi289 – 291Combined sources3
Turni292 – 296Combined sources5
Beta strandi304 – 307Combined sources4
Helixi315 – 323Combined sources9
Beta strandi330 – 339Combined sources10
Beta strandi341 – 347Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SOTX-ray2.30A/B/C43-355[»]
1SOZX-ray2.40A/B/C43-355[»]
1TE0X-ray2.20A/B37-354[»]
1VCWX-ray3.05A/B/C43-355[»]
2QF0X-ray2.50A/B/C/D/E/F/G/H/I27-256[»]
2QF3X-ray2.04A/B/C27-256[»]
2QGRX-ray2.70A27-256[»]
2R3UX-ray2.60A/B/C43-252[»]
2R3YX-ray2.50A/B/C43-355[»]
2RCEX-ray2.35A/B/C/D/E/F/G/H/I27-256[»]
3B8JX-ray2.51A27-256[»]
3GCNX-ray3.00A27-355[»]
3GCOX-ray2.80A27-355[»]
3GDSX-ray2.85A27-355[»]
3GDUX-ray3.00A/B/C27-355[»]
3GDVX-ray2.49A/B/C27-355[»]
3LGIX-ray1.65A/B/C27-256[»]
3LGTX-ray2.68A27-256[»]
3LGUX-ray2.46A27-256[»]
3LGVX-ray2.73A/B/C/D/E/F/G/H/I27-256[»]
3LGWX-ray2.50A27-256[»]
3LGYX-ray2.70A27-256[»]
3LH1X-ray2.51A27-256[»]
3LH3X-ray2.35A/B/C/D/E/F/G/H/I27-256[»]
4RQYX-ray2.20A/B37-355[»]
4RQZX-ray2.40A/B/C43-355[»]
4RR0X-ray3.05A/B/C43-355[»]
4RR1X-ray2.30A/B/C43-355[»]
ProteinModelPortaliP0AEE3.
SMRiP0AEE3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AEE3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini281 – 326PDZPROSITE-ProRule annotationAdd BLAST46

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni259 – 264Substrate binding6

Domaini

The PDZ domain probably binds peptides ending with C-terminal Tyr-X-Phe sequences, which activates proteolysis. In the absence of OMP peptides the PDZ domain inhibits peptidase activity.2 Publications

Sequence similaritiesi

Belongs to the peptidase S1C family.Curated
Contains 1 PDZ (DHR) domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105C0H. Bacteria.
COG0265. LUCA.
HOGENOMiHOG000223641.
InParanoidiP0AEE3.
KOiK04691.
OMAiVYNQAND.
PhylomeDBiP0AEE3.

Family and domain databases

Gene3Di2.30.42.10. 1 hit.
InterProiIPR001478. PDZ.
IPR011783. Pept_S1C_DegS.
IPR009003. Peptidase_S1_PA.
IPR001940. Peptidase_S1C.
[Graphical view]
PfamiPF13180. PDZ_2. 1 hit.
[Graphical view]
PRINTSiPR00834. PROTEASES2C.
SMARTiSM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
SSF50494. SSF50494. 1 hit.
TIGRFAMsiTIGR02038. protease_degS. 1 hit.
PROSITEiPS50106. PDZ. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AEE3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFVKLLRSVA IGLIVGAILL VAMPSLRSLN PLSTPQFDST DETPASYNLA
60 70 80 90 100
VRRAAPAVVN VYNRGLNTNS HNQLEIRTLG SGVIMDQRGY IITNKHVIND
110 120 130 140 150
ADQIIVALQD GRVFEALLVG SDSLTDLAVL KINATGGLPT IPINARRVPH
160 170 180 190 200
IGDVVLAIGN PYNLGQTITQ GIISATGRIG LNPTGRQNFL QTDASINHGN
210 220 230 240 250
SGGALVNSLG ELMGINTLSF DKSNDGETPE GIGFAIPFQL ATKIMDKLIR
260 270 280 290 300
DGRVIRGYIG IGGREIAPLH AQGGGIDQLQ GIVVNEVSPD GPAANAGIQV
310 320 330 340 350
NDLIISVDNK PAISALETMD QVAEIRPGSV IPVVVMRDDK QLTLQVTIQE

YPATN
Length:355
Mass (Da):37,581
Last modified:December 6, 2005 - v1
Checksum:iD091B4D65E8FE1CC
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti253R → A in M24777 (PubMed:3322223).Curated1
Sequence conflicti307V → E in M24777 (PubMed:3322223).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U15661 Genomic DNA. Translation: AAC43993.1.
U32495 Genomic DNA. Translation: AAC44006.1.
U18997 Genomic DNA. Translation: AAA58037.1.
U00096 Genomic DNA. Translation: AAC76267.1.
AP009048 Genomic DNA. Translation: BAE77278.1.
M24777 Unassigned DNA. No translation available.
PIRiJC6052.
RefSeqiNP_417702.1. NC_000913.3.
WP_000497723.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76267; AAC76267; b3235.
BAE77278; BAE77278; BAE77278.
GeneIDi947865.
KEGGiecj:JW3204.
eco:b3235.
PATRICi32121896. VBIEscCol129921_3332.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U15661 Genomic DNA. Translation: AAC43993.1.
U32495 Genomic DNA. Translation: AAC44006.1.
U18997 Genomic DNA. Translation: AAA58037.1.
U00096 Genomic DNA. Translation: AAC76267.1.
AP009048 Genomic DNA. Translation: BAE77278.1.
M24777 Unassigned DNA. No translation available.
PIRiJC6052.
RefSeqiNP_417702.1. NC_000913.3.
WP_000497723.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SOTX-ray2.30A/B/C43-355[»]
1SOZX-ray2.40A/B/C43-355[»]
1TE0X-ray2.20A/B37-354[»]
1VCWX-ray3.05A/B/C43-355[»]
2QF0X-ray2.50A/B/C/D/E/F/G/H/I27-256[»]
2QF3X-ray2.04A/B/C27-256[»]
2QGRX-ray2.70A27-256[»]
2R3UX-ray2.60A/B/C43-252[»]
2R3YX-ray2.50A/B/C43-355[»]
2RCEX-ray2.35A/B/C/D/E/F/G/H/I27-256[»]
3B8JX-ray2.51A27-256[»]
3GCNX-ray3.00A27-355[»]
3GCOX-ray2.80A27-355[»]
3GDSX-ray2.85A27-355[»]
3GDUX-ray3.00A/B/C27-355[»]
3GDVX-ray2.49A/B/C27-355[»]
3LGIX-ray1.65A/B/C27-256[»]
3LGTX-ray2.68A27-256[»]
3LGUX-ray2.46A27-256[»]
3LGVX-ray2.73A/B/C/D/E/F/G/H/I27-256[»]
3LGWX-ray2.50A27-256[»]
3LGYX-ray2.70A27-256[»]
3LH1X-ray2.51A27-256[»]
3LH3X-ray2.35A/B/C/D/E/F/G/H/I27-256[»]
4RQYX-ray2.20A/B37-355[»]
4RQZX-ray2.40A/B/C43-355[»]
4RR0X-ray3.05A/B/C43-355[»]
4RR1X-ray2.30A/B/C43-355[»]
ProteinModelPortaliP0AEE3.
SMRiP0AEE3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-39580N.
IntActiP0AEE3. 3 interactors.
STRINGi511145.b3235.

Protein family/group databases

MEROPSiS01.275.

Proteomic databases

PaxDbiP0AEE3.
PRIDEiP0AEE3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76267; AAC76267; b3235.
BAE77278; BAE77278; BAE77278.
GeneIDi947865.
KEGGiecj:JW3204.
eco:b3235.
PATRICi32121896. VBIEscCol129921_3332.

Organism-specific databases

EchoBASEiEB1605.
EcoGeneiEG11652. degS.

Phylogenomic databases

eggNOGiENOG4105C0H. Bacteria.
COG0265. LUCA.
HOGENOMiHOG000223641.
InParanoidiP0AEE3.
KOiK04691.
OMAiVYNQAND.
PhylomeDBiP0AEE3.

Enzyme and pathway databases

BioCyciEcoCyc:EG11652-MONOMER.
ECOL316407:JW3204-MONOMER.
MetaCyc:EG11652-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AEE3.
PROiP0AEE3.

Family and domain databases

Gene3Di2.30.42.10. 1 hit.
InterProiIPR001478. PDZ.
IPR011783. Pept_S1C_DegS.
IPR009003. Peptidase_S1_PA.
IPR001940. Peptidase_S1C.
[Graphical view]
PfamiPF13180. PDZ_2. 1 hit.
[Graphical view]
PRINTSiPR00834. PROTEASES2C.
SMARTiSM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
SSF50494. SSF50494. 1 hit.
TIGRFAMsiTIGR02038. protease_degS. 1 hit.
PROSITEiPS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDEGS_ECOLI
AccessioniPrimary (citable) accession number: P0AEE3
Secondary accession number(s): P31137, Q2M8X8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: December 6, 2005
Last modified: November 2, 2016
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Regulated intramembrane proteolysis (RIP) occurs when an extracytoplasmic signal triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. A membrane-spanning regulatory substrate protein is first cut extracytoplasmically (site-1 protease, S1P, this enzyme), then within the membrane itself (site-2 protease, S2P), while cytoplasmic proteases finish degrading the regulatory protein, liberating the effector protein.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.