Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Response regulator PleD

Gene

pleD

Organism
Caulobacter crescentus (strain NA1000 / CB15N)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition.
Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger.

Catalytic activityi

2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.

Cofactori

Mg2+1 PublicationNote: Binds 2 Mg2+ per monomer.1 Publication

Enzyme regulationi

Allosterically inhibited by dimers of the product c-di-GMP.

Pathwayi: 3',5'-cyclic di-GMP biosynthesis

This protein is involved in the pathway 3',5'-cyclic di-GMP biosynthesis, which is part of Purine metabolism.
View all proteins of this organism that are known to be involved in the pathway 3',5'-cyclic di-GMP biosynthesis and in Purine metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Magnesium 1
Metal bindingi10 – 101Magnesium 1
Metal bindingi53 – 531Magnesium 1
Metal bindingi55 – 551Magnesium 1; via carbonyl oxygen
Sitei178 – 1781Allosteric product binding, non-activate state
Sitei313 – 3131Allosteric product binding, active state
Metal bindingi327 – 3271Magnesium 2
Metal bindingi328 – 3281Magnesium 2; via carbonyl oxygen
Sitei332 – 3321Transition state stabilizerSequence analysis
Binding sitei335 – 3351Substrate
Binding sitei344 – 3441Substrate
Sitei359 – 3591Allosteric product phosphate group binding, activate and inactive state
Sitei362 – 3621Allosteric product binding, activate and inactive state
Active sitei370 – 3701Proton acceptorSequence analysis
Metal bindingi370 – 3701Magnesium 2
Sitei390 – 3901Allosteric product binding, activate and inactive state

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Transducer, Transferase

Keywords - Biological processi

Cell cycle, Differentiation, Two-component regulatory system

Keywords - Ligandi

GTP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciCAULONA1000:CCNA_02546-MONOMER.
RETL1328306-WGS:GSTH-1656-MONOMER.
UniPathwayiUPA00599.

Names & Taxonomyi

Protein namesi
Recommended name:
Response regulator PleD
Alternative name(s):
Stalked cell differentiation-controlling protein
Including the following 1 domains:
Diguanylate cyclase (EC:2.7.7.65)
Short name:
DGC
Alternative name(s):
Diguanylate kinase
Gene namesi
Name:pleD
Ordered Locus Names:CCNA_02546
OrganismiCaulobacter crescentus (strain NA1000 / CB15N)
Taxonomic identifieri565050 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
Proteomesi
  • UP000001364 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm

  • Note: Phosphorylated PleD localizes to the differentiating pole.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 454454Response regulator PleDPRO_0000396955Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei53 – 5314-aspartylphosphatePROSITE-ProRule annotation2 Publications

Post-translational modificationi

Phosphorylated by PleC and DivJ. Phosphorylation stimulates cyclase activity.2 Publications

Keywords - PTMi

Phosphoprotein

Interactioni

Subunit structurei

Homodimer. Inactive monomer in solution, dimerization seems to be required for activity. Dimerization in vitro is enhanced by BeF3- and by 1 mM Mn2+ or 10 mM Mg2+.1 Publication

Structurei

Secondary structure

1
454
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 85Combined sources
Helixi14 – 2411Combined sources
Beta strandi28 – 347Combined sources
Helixi35 – 4511Combined sources
Beta strandi48 – 547Combined sources
Beta strandi57 – 593Combined sources
Helixi61 – 7010Combined sources
Turni72 – 765Combined sources
Beta strandi79 – 835Combined sources
Helixi88 – 9710Combined sources
Beta strandi101 – 1066Combined sources
Helixi109 – 13325Combined sources
Turni134 – 1374Combined sources
Turni140 – 1434Combined sources
Helixi146 – 1483Combined sources
Beta strandi151 – 1533Combined sources
Beta strandi155 – 1595Combined sources
Helixi163 – 17311Combined sources
Turni174 – 1763Combined sources
Beta strandi177 – 1826Combined sources
Helixi185 – 1939Combined sources
Beta strandi197 – 2026Combined sources
Beta strandi206 – 2083Combined sources
Helixi210 – 2189Combined sources
Helixi221 – 2233Combined sources
Beta strandi228 – 2325Combined sources
Helixi237 – 2459Combined sources
Beta strandi250 – 2556Combined sources
Helixi258 – 27922Combined sources
Beta strandi280 – 2834Combined sources
Helixi284 – 2863Combined sources
Beta strandi289 – 2913Combined sources
Turni293 – 2953Combined sources
Helixi300 – 31516Combined sources
Beta strandi322 – 3287Combined sources
Helixi331 – 3377Combined sources
Helixi340 – 35617Combined sources
Beta strandi362 – 3665Combined sources
Beta strandi368 – 3769Combined sources
Helixi381 – 39616Combined sources
Beta strandi400 – 4023Combined sources
Helixi403 – 4053Combined sources
Beta strandi407 – 4093Combined sources
Beta strandi413 – 4197Combined sources
Helixi427 – 44317Combined sources
Beta strandi449 – 4513Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W25X-ray2.70A/B2-454[»]
2V0NX-ray2.71A/B2-454[»]
2WB4X-ray2.80A/B1-454[»]
ProteinModelPortaliB8GZM2.
SMRiB8GZM2. Positions 2-454.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiB8GZM2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 120117Response regulatory 1PROSITE-ProRule annotationAdd
BLAST
Domaini155 – 269115Response regulatory 2PROSITE-ProRule annotationAdd
BLAST
Domaini319 – 454136GGDEFPROSITE-ProRule annotationAdd
BLAST

Domaini

Activated by phosphorylation at the first response regulatory domain, which induces dimerization mediated by the two response regulatory domains and allows the two substrate-binding sites to approach each other and the condensation reaction to occur (Probable). The diguanylate cyclase activity is harbored by the GGDEF domain.Curated

Sequence similaritiesi

Contains 1 GGDEF domain.PROSITE-ProRule annotation
Contains 2 response regulatory domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000167204.
KOiK02488.
OMAiIRRKRYN.
OrthoDBiPOG091H049G.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR011006. CheY-like_superfamily.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR001789. Sig_transdc_resp-reg_receiver.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF00072. Response_reg. 2 hits.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
SM00448. REC. 2 hits.
[Graphical view]
SUPFAMiSSF52172. SSF52172. 2 hits.
SSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50110. RESPONSE_REGULATORY. 2 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

B8GZM2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSARILVVDD IEANVRLLEA KLTAEYYEVS TAMDGPTALA MAARDLPDII
60 70 80 90 100
LLDVMMPGMD GFTVCRKLKD DPTTRHIPVV LITALDGRGD RIQGLESGAS
110 120 130 140 150
DFLTKPIDDV MLFARVRSLT RFKLVIDELR QREASGRRMG VIAGAAARLD
160 170 180 190 200
GLGGRVLIVD DNERQAQRVA AELGVEHRPV IESDPEKAKI SAGGPVDLVI
210 220 230 240 250
VNAAAKNFDG LRFTAALRSE ERTRQLPVLA MVDPDDRGRM VKALEIGVND
260 270 280 290 300
ILSRPIDPQE LSARVKTQIQ RKRYTDYLRN NLDHSLELAV TDQLTGLHNR
310 320 330 340 350
RYMTGQLDSL VKRATLGGDP VSALLIDIDF FKKINDTFGH DIGDEVLREF
360 370 380 390 400
ALRLASNVRA IDLPCRYGGE EFVVIMPDTA LADALRIAER IRMHVSGSPF
410 420 430 440 450
TVAHGREMLN VTISIGVSAT AGEGDTPEAL LKRADEGVYQ AKASGRNAVV

GKAA
Length:454
Mass (Da):49,624
Last modified:March 3, 2009 - v1
Checksum:iD44909D42B581516
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001340 Genomic DNA. Translation: ACL96011.1.
RefSeqiWP_010920320.1. NC_011916.1.
YP_002517919.1. NC_011916.1.

Genome annotation databases

EnsemblBacteriaiACL96011; ACL96011; CCNA_02546.
GeneIDi7333643.
KEGGiccs:CCNA_02546.
PATRICi21309637. VBICauCre52860_2497.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001340 Genomic DNA. Translation: ACL96011.1.
RefSeqiWP_010920320.1. NC_011916.1.
YP_002517919.1. NC_011916.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1W25X-ray2.70A/B2-454[»]
2V0NX-ray2.71A/B2-454[»]
2WB4X-ray2.80A/B1-454[»]
ProteinModelPortaliB8GZM2.
SMRiB8GZM2. Positions 2-454.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACL96011; ACL96011; CCNA_02546.
GeneIDi7333643.
KEGGiccs:CCNA_02546.
PATRICi21309637. VBICauCre52860_2497.

Phylogenomic databases

HOGENOMiHOG000167204.
KOiK02488.
OMAiIRRKRYN.
OrthoDBiPOG091H049G.

Enzyme and pathway databases

UniPathwayiUPA00599.
BioCyciCAULONA1000:CCNA_02546-MONOMER.
RETL1328306-WGS:GSTH-1656-MONOMER.

Miscellaneous databases

EvolutionaryTraceiB8GZM2.

Family and domain databases

CDDicd01949. GGDEF. 1 hit.
InterProiIPR011006. CheY-like_superfamily.
IPR000160. GGDEF_dom.
IPR029787. Nucleotide_cyclase.
IPR001789. Sig_transdc_resp-reg_receiver.
[Graphical view]
PfamiPF00990. GGDEF. 1 hit.
PF00072. Response_reg. 2 hits.
[Graphical view]
SMARTiSM00267. GGDEF. 1 hit.
SM00448. REC. 2 hits.
[Graphical view]
SUPFAMiSSF52172. SSF52172. 2 hits.
SSF55073. SSF55073. 1 hit.
TIGRFAMsiTIGR00254. GGDEF. 1 hit.
PROSITEiPS50887. GGDEF. 1 hit.
PS50110. RESPONSE_REGULATORY. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPLED_CAUCN
AccessioniPrimary (citable) accession number: B8GZM2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: March 3, 2009
Last modified: September 7, 2016
This is version 56 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

3D-structure, Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.