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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)DescriptionActionsGraphical viewLength
Metal bindingi9Magnesium 11
Metal bindingi10Magnesium 11
Metal bindingi53Magnesium 11
Metal bindingi55Magnesium 1; via carbonyl oxygen1
Sitei178Allosteric product binding, non-activate state1
Sitei313Allosteric product binding, active state1
Metal bindingi327Magnesium 21
Metal bindingi328Magnesium 2; via carbonyl oxygen1
Sitei332Transition state stabilizerSequence analysis1
Binding sitei335Substrate1
Binding sitei344Substrate1
Sitei359Allosteric product phosphate group binding, activate and inactive state1
Sitei362Allosteric product binding, activate and inactive state1
Active sitei370Proton acceptorSequence analysis1
Metal bindingi370Magnesium 21
Sitei390Allosteric product binding, activate and inactive state1

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.
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)DescriptionActionsGraphical viewLength
ChainiPRO_00003969551 – 454Response regulator PleDAdd BLAST454

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei534-aspartylphosphatePROSITE-ProRule annotation2 Publications1

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

1454
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 8Combined sources5
Helixi14 – 24Combined sources11
Beta strandi28 – 34Combined sources7
Helixi35 – 45Combined sources11
Beta strandi48 – 54Combined sources7
Beta strandi57 – 59Combined sources3
Helixi61 – 70Combined sources10
Turni72 – 76Combined sources5
Beta strandi79 – 83Combined sources5
Helixi88 – 97Combined sources10
Beta strandi101 – 106Combined sources6
Helixi109 – 133Combined sources25
Turni134 – 137Combined sources4
Turni140 – 143Combined sources4
Helixi146 – 148Combined sources3
Beta strandi151 – 153Combined sources3
Beta strandi155 – 159Combined sources5
Helixi163 – 173Combined sources11
Turni174 – 176Combined sources3
Beta strandi177 – 182Combined sources6
Helixi185 – 193Combined sources9
Beta strandi197 – 202Combined sources6
Beta strandi206 – 208Combined sources3
Helixi210 – 218Combined sources9
Helixi221 – 223Combined sources3
Beta strandi228 – 232Combined sources5
Helixi237 – 245Combined sources9
Beta strandi250 – 255Combined sources6
Helixi258 – 279Combined sources22
Beta strandi280 – 283Combined sources4
Helixi284 – 286Combined sources3
Beta strandi289 – 291Combined sources3
Turni293 – 295Combined sources3
Helixi300 – 315Combined sources16
Beta strandi322 – 328Combined sources7
Helixi331 – 337Combined sources7
Helixi340 – 356Combined sources17
Beta strandi362 – 366Combined sources5
Beta strandi368 – 376Combined sources9
Helixi381 – 396Combined sources16
Beta strandi400 – 402Combined sources3
Helixi403 – 405Combined sources3
Beta strandi407 – 409Combined sources3
Beta strandi413 – 419Combined sources7
Helixi427 – 443Combined sources17
Beta strandi449 – 451Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiB8GZM2.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini4 – 120Response regulatory 1PROSITE-ProRule annotationAdd BLAST117
Domaini155 – 269Response regulatory 2PROSITE-ProRule annotationAdd BLAST115
Domaini319 – 454GGDEFPROSITE-ProRule annotationAdd BLAST136

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1W25X-ray2.70A/B2-454[»]
2V0NX-ray2.71A/B2-454[»]
2WB4X-ray2.80A/B1-454[»]
ProteinModelPortaliB8GZM2.
SMRiB8GZM2.
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.

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: November 2, 2016
This is version 58 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.