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Protein

Cyclic di-GMP phosphodiesterase Gmr

Gene

gmr

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Part of a 2 protein system that seems to be dedicated to transcription of csgD. This protein decreases csgD transcription and thus decreases expression of adhesive curli fimbriae genes csgEFG, csgBAC/ymaD and adrA (yaic). Activity of this protein is antagonized by the diguanylate cyclase YdaM. In vitro has c-di-GMP phosphodiesterase activity. Cyclic-di-GMP is a second messenger which controls cell surface-associated traits in bacteria.1 Publication

Catalytic activityi

Cyclic di-3',5'-guanylate + H2O = 5'-phosphoguanylyl(3'->5')guanosine.1 Publication

GO - Molecular functioni

  • cyclic-guanylate-specific phosphodiesterase activity Source: EcoCyc
  • GTP binding Source: EcoCyc

GO - Biological processi

  • negative regulation of cyclase activity Source: EcoCyc
  • posttranscriptional regulation of gene expression Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

c-di-GMP

Enzyme and pathway databases

BioCyciEcoCyc:G6639-MONOMER.
ECOL316407:JW1278-MONOMER.
MetaCyc:G6639-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic di-GMP phosphodiesterase Gmr (EC:3.1.4.52)
Gene namesi
Name:gmr
Synonyms:yciR
Ordered Locus Names:b1285, JW1278
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13415. gmr.

Pathology & Biotechi

Disruption phenotypei

Leads to overproduction of curli fimbrae and autoaggregation in cultures grown at 28 degrees Celsius.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 661661Cyclic di-GMP phosphodiesterase GmrPRO_0000168885Add
BLAST

Proteomic databases

PaxDbiP77334.

Expressioni

Inductioni

Constitutively expressed at both 28 and 37 degrees Celsius, during transition into stationary phase, more highly expressed on plates than in liquid medium. Expression is RpoS dependent and repressed by H-NS.2 Publications

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
mlrAP333582EBI-548149,EBI-1127668
ydaMP773025EBI-548149,EBI-544662

Protein-protein interaction databases

BioGridi4261961. 15 interactions.
DIPiDIP-11590N.
IntActiP77334. 6 interactions.
MINTiMINT-1265402.
STRINGi511145.b1285.

Structurei

3D structure databases

ProteinModelPortaliP77334.
SMRiP77334. Positions 236-654.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini109 – 17971PASPROSITE-ProRule annotationAdd
BLAST
Domaini265 – 397133GGDEFPROSITE-ProRule annotationAdd
BLAST
Domaini406 – 658253EALPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 EAL domain.PROSITE-ProRule annotation
Contains 1 GGDEF domain.PROSITE-ProRule annotation
Contains 1 PAS (PER-ARNT-SIM) domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
COG2199. LUCA.
COG2200. LUCA.
COG2202. LUCA.
HOGENOMiHOG000136248.
InParanoidiP77334.
KOiK14051.
OMAiYTGLKEQ.
OrthoDBiEOG69GZGV.
PhylomeDBiP77334.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR000014. PAS.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF00990. GGDEF. 1 hit.
PF13426. PAS_9. 1 hit.
[Graphical view]
SMARTiSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
SM00091. PAS. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
TIGR00229. sensory_box. 1 hit.
PROSITEiPS50883. EAL. 1 hit.
PS50887. GGDEF. 1 hit.
PS50112. PAS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P77334-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKTVRESTTL YNFLGSHNPY WRLTESSDVL RFSTTETTEP DRTLQLSAEQ
60 70 80 90 100
AARIREMTVI TSSLMMSLTV DESDLSVHLV GRKINKREWA GNASAWHDTP
110 120 130 140 150
AVARDLSHGL SFAEQVVSEA HSAIVILDSR GNIQRFNRLC EDYTGLKEHD
160 170 180 190 200
VIGQSVFKLF MSRREAAASR RNNRVFFRSG NAYEVELWIP TCKGQRLFLF
210 220 230 240 250
RNKFVHSGSG KNEIFLICSG TDITEERRAQ ERLRILANTD SITGLPNRNA
260 270 280 290 300
MQDLIDHAIN HADNNKVGVV YLDLDNFKKV NDAYGHLFGD QLLRDVSLAI
310 320 330 340 350
LSCLEHDQVL ARPGGDEFLV LASNTSQSAL EAMASRILTR LRLPFRIGLI
360 370 380 390 400
EVYTSCSVGI ALSPEHGSDS TAIIRHADTA MYTAKEGGRG QFCVFTPEMN
410 420 430 440 450
QRVFEYLWLD TNLRKALEND QLVIHYQPKI TWRGEVRSLE ALVRWQSPER
460 470 480 490 500
GLIPPLDFIS YAEESGLIVP LGRWVILDVV RQVAKWRDKG INLRVAVNIS
510 520 530 540 550
ARQLADQTIF TALKQVLQEL NFEYCPIDVE LTESCLIEND ELALSVIQQF
560 570 580 590 600
SQLGAQVHLD DFGTGYSSLS QLARFPIDAI KLDQVFVRDI HKQPVSQSLV
610 620 630 640 650
RAIVAVAQAL NLQVIAEGVE SAKEDAFLTK NGINERQGFL FAKPMPAVAF
660
ERWYKRYLKR A
Length:661
Mass (Da):74,665
Last modified:February 1, 1997 - v1
Checksum:i991D47CDE46A8F01
GO

Sequence cautioni

The sequence L40788 differs from that shown. Reason: Frameshift at positions 5, 25, 365, 392 and 451. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41V → L in L40788 (Ref. 4) Curated
Sequence conflicti113 – 1131A → P in L40788 (Ref. 4) Curated
Sequence conflicti175 – 1751V → L in L40788 (Ref. 4) Curated
Sequence conflicti256 – 2561D → H in L40788 (Ref. 4) Curated
Sequence conflicti344 – 3441P → G in L40788 (Ref. 4) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74367.1.
AP009048 Genomic DNA. Translation: BAA14839.1.
L40788 Genomic DNA. No translation available.
PIRiH64876.
RefSeqiNP_415801.1. NC_000913.3.
WP_000859945.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74367; AAC74367; b1285.
BAA14839; BAA14839; BAA14839.
GeneIDi945868.
KEGGiecj:JW1278.
eco:b1285.
PATRICi32117836. VBIEscCol129921_1338.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74367.1.
AP009048 Genomic DNA. Translation: BAA14839.1.
L40788 Genomic DNA. No translation available.
PIRiH64876.
RefSeqiNP_415801.1. NC_000913.3.
WP_000859945.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP77334.
SMRiP77334. Positions 236-654.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261961. 15 interactions.
DIPiDIP-11590N.
IntActiP77334. 6 interactions.
MINTiMINT-1265402.
STRINGi511145.b1285.

Proteomic databases

PaxDbiP77334.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74367; AAC74367; b1285.
BAA14839; BAA14839; BAA14839.
GeneIDi945868.
KEGGiecj:JW1278.
eco:b1285.
PATRICi32117836. VBIEscCol129921_1338.

Organism-specific databases

EchoBASEiEB3191.
EcoGeneiEG13415. gmr.

Phylogenomic databases

eggNOGiENOG4105BZU. Bacteria.
COG2199. LUCA.
COG2200. LUCA.
COG2202. LUCA.
HOGENOMiHOG000136248.
InParanoidiP77334.
KOiK14051.
OMAiYTGLKEQ.
OrthoDBiEOG69GZGV.
PhylomeDBiP77334.

Enzyme and pathway databases

BioCyciEcoCyc:G6639-MONOMER.
ECOL316407:JW1278-MONOMER.
MetaCyc:G6639-MONOMER.

Miscellaneous databases

PROiP77334.

Family and domain databases

Gene3Di3.20.20.450. 1 hit.
InterProiIPR001633. EAL_dom.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR000014. PAS.
[Graphical view]
PfamiPF00563. EAL. 1 hit.
PF00990. GGDEF. 1 hit.
PF13426. PAS_9. 1 hit.
[Graphical view]
SMARTiSM00052. EAL. 1 hit.
SM00267. GGDEF. 1 hit.
SM00091. PAS. 1 hit.
[Graphical view]
SUPFAMiSSF141868. SSF141868. 1 hit.
SSF55073. SSF55073. 1 hit.
SSF55785. SSF55785. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
TIGR00229. sensory_box. 1 hit.
PROSITEiPS50883. EAL. 1 hit.
PS50887. GGDEF. 1 hit.
PS50112. PAS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. Rita Z.R., Arraiano C.A.
    Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-557.
  5. "Cyclic-di-GMP-mediated signalling within the sigma network of Escherichia coli."
    Weber H., Pesavento C., Possling A., Tischendorf G., Hengge R.
    Mol. Microbiol. 62:1014-1034(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, FUNCTION, INDUCTION, RPOS-DEPENDENCE, H-NS-REPRESSION, DISRUPTION PHENOTYPE.
    Strain: K12 / MC4100.
  6. "Gene expression patterns and differential input into curli fimbriae regulation of all GGDEF/EAL domain proteins in Escherichia coli."
    Sommerfeldt N., Possling A., Becker G., Pesavento C., Tschowri N., Hengge R.
    Microbiology 155:1318-1331(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION, RPOS-DEPENDENCE.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.

Entry informationi

Entry nameiGMR_ECOLI
AccessioniPrimary (citable) accession number: P77334
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: January 20, 2016
This is version 132 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.