Response regulator PleD - Caulobacter crescentus (strain NA1000 / CB15N)

Contribute

Send feedback

Read comments (?) or add your own

B8GZM2 (PLED_CAUCN) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 37. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

text xml rdf/xml gff fasta

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Response regulator PleD

Alternative name(s):
Stalked cell differentiation-controlling protein

Including the following 1 domains:

Diguanylate cyclase
Short name=DGC
EC=2.7.7.65
Alternative name(s):
Diguanylate kinase

Gene names

Name:	pleD
Ordered Locus Names:	CCNA_02546

Organism

Caulobacter crescentus (strain NA1000 / CB15N) [Complete proteome] [HAMAP]

Taxonomic identifier

565050 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Alphaproteobacteria › Caulobacterales › Caulobacteraceae › Caulobacter ›

Protein attributes

Sequence length	454 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Response regulator that is part of a signal transduction pathway controlling cell differentiation in the swarmer-to-stalked cell transition. Ref.2 Ref.3 Catalyzes the condensation of two GTP molecules to the cyclic dinucleotide di-GMP (c-di-GMP), which acts as a secondary messenger. Ref.2 Ref.3
Catalytic activity	2 GTP = 2 diphosphate + cyclic di-3',5'-guanylate.
Cofactor	Binds 2 Mg²⁺ per monomer. Ref.5
Enzyme regulation	Allosterically inhibited by dimers of the product c-di-GMP.
Pathway	Purine metabolism; 3',5'-cyclic di-GMP biosynthesis.
Subunit structure	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⁺. Ref.4
Subcellular location	Cytoplasm. Note: Phosphorylated PleD localizes to the differentiating pole.
Domain	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.
Post-translational modification	Phosphorylated by PleC and DivJ. Phosphorylation stimulates cyclase activity. Ref.2 Ref.3
Sequence similarities	Contains 1 GGDEF domain. Contains 2 response regulatory domains.

Ontologies

Keywords
Biological process	Cell cycle Differentiation Two-component regulatory system
Cellular component	Cytoplasm
Domain	Repeat
Ligand	GTP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Transducer Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological_process	cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW cyclic nucleotide biosynthetic process Inferred from electronic annotation. Source: InterPro regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	GTP binding Inferred from electronic annotation. Source: UniProtKB-KW diguanylate cyclase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphorelay response regulator activity Inferred from electronic annotation. Source: InterPro phosphorus-oxygen lyase activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 454

454

Response regulator PleD

PRO_0000396955

Regions

Domain

4 – 120

117

Response regulatory 1

Domain

155 – 269

115

Response regulatory 2

Domain

319 – 454

136

GGDEF

Sites

Active site

370

Proton acceptor Potential

Metal binding

Magnesium 1

Metal binding

Magnesium 1

Metal binding

Magnesium 1

Metal binding

Magnesium 1; via carbonyl oxygen

Metal binding

327

Magnesium 2

Metal binding

328

Magnesium 2; via carbonyl oxygen

Metal binding

370

Magnesium 2

Binding site

335

Substrate

Binding site

344

Substrate

Site

178

Allosteric product binding, non-activate state

Site

313

Allosteric product binding, active state

Site

332

Transition state stabilizer Potential

Site

359

Allosteric product phosphate group binding, activate and inactive state

Site

362

Allosteric product binding, activate and inactive state

Site

390

Allosteric product binding, activate and inactive state

Amino acid modifications

Modified residue

4-aspartylphosphate

Secondary structure

454

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

B8GZM2 [UniParc].

Last modified March 3, 2009. Version 1.
Checksum: D44909D42B581516
Show »

FASTA

454

49,624

        10         20         30         40         50         60 
MSARILVVDD IEANVRLLEA KLTAEYYEVS TAMDGPTALA MAARDLPDII LLDVMMPGMD 

        70         80         90        100        110        120 
GFTVCRKLKD DPTTRHIPVV LITALDGRGD RIQGLESGAS DFLTKPIDDV MLFARVRSLT 

       130        140        150        160        170        180 
RFKLVIDELR QREASGRRMG VIAGAAARLD GLGGRVLIVD DNERQAQRVA AELGVEHRPV 

       190        200        210        220        230        240 
IESDPEKAKI SAGGPVDLVI VNAAAKNFDG LRFTAALRSE ERTRQLPVLA MVDPDDRGRM 

       250        260        270        280        290        300 
VKALEIGVND ILSRPIDPQE LSARVKTQIQ RKRYTDYLRN NLDHSLELAV TDQLTGLHNR 

       310        320        330        340        350        360 
RYMTGQLDSL VKRATLGGDP VSALLIDIDF FKKINDTFGH DIGDEVLREF ALRLASNVRA 

       370        380        390        400        410        420 
IDLPCRYGGE EFVVIMPDTA LADALRIAER IRMHVSGSPF TVAHGREMLN VTISIGVSAT 

       430        440        450 
AGEGDTPEAL LKRADEGVYQ AKASGRNAVV GKAA

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The genetic basis of laboratory adaptation in Caulobacter crescentus." Marks M.E., Castro-Rojas C.M., Teiling C., Du L., Kapatral V., Walunas T.L., Crosson S. J. Bacteriol. 192:3678-3688(2010) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: NA1000 / CB15N.
[2]	"Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus." Aldridge P., Paul R., Goymer P., Rainey P., Jenal U. Mol. Microbiol. 47:1695-1708(2003) [PubMed] [Europe PMC] [Abstract] Cited for: ROLE IN POLAR DEVELOPMENT, PHOSPHORYLATION.
[3]	"Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain." Paul R., Weiser S., Amiot N.C., Chan C., Schirmer T., Giese B., Jenal U. Genes Dev. 18:715-727(2004) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS A NUCLEOTIDE CYCLASE, CELL POLE LOCALIZATION, PHOSPHORYLATION.
[4]	"Structural basis of activity and allosteric control of diguanylate cyclase." Chan C., Paul R., Samoray D., Amiot N.C., Giese B., Jenal U., Schirmer T. Proc. Natl. Acad. Sci. U.S.A. 101:17084-17089(2004) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF COMPLEX WITH C-DI-GMP, ALLOSTERIC REGULATION, SUBUNIT.
[5]	"Structure of BeF(3-)-modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition." Wassmann P., Chan C., Paul R., Beck A., Heerklotz H., Jenal U., Schirmer T. Structure 15:915-927(2007) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.71 ANGSTROMS) OF 2-454 OF DIMER WITH C-DI-GMP IN THE ACTIVATED FORM, COFACTOR.
[6]	"Crystal structure of activated Pled, identification of dimerization and catalysis relevant regulatory mechanisms." Wassmann P., Massa C., Zaehringer F., Schirmer T. Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

CP001340 Genomic DNA. Translation: ACL96011.1.

RefSeq

YP_002517919.1. NC_011916.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1W25	X-ray	2.70	A/B	2-454	[»]
2V0N	X-ray	2.71	A/B	2-454	[»]
2WB4	X-ray	2.80	A/B	1-454	[»]

ProteinModelPortal

B8GZM2.

SMR

B8GZM2. Positions 2-454.

ModBase

Search...

Protein-protein interaction databases

STRING

190650.CC_2462.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

ACL96011; ACL96011; CCNA_02546.

GeneID

7333643.

KEGG

ccs:CCNA_02546.

PATRIC

21309637. VBICauCre52860_2497.

Organism-specific databases

CMR

Search...

Phylogenomic databases

eggNOG

COG3706.

HOGENOM

HOG000167204.

K02488.

OMA

LAICERN.

ProtClustDB

PRK09581.

Enzyme and pathway databases

UniPathway

UPA00599.

Family and domain databases

InterPro

IPR001054. A/G_cyclase.
IPR011006. CheY-like_superfamily.
IPR000160. GGDEF_dom.
IPR001789. Sig_transdc_resp-reg_receiver.
[Graphical view]

Pfam

PF00990. GGDEF. 1 hit.
PF00072. Response_reg. 2 hits.
[Graphical view]

SMART

SM00267. GGDEF. 1 hit.
SM00448. REC. 2 hits.
[Graphical view]

SUPFAM

SSF55073. A/G_cyclase. 1 hit.
SSF52172. CheY_like. 2 hits.

TIGRFAMs

TIGR00254. GGDEF. 1 hit.

PROSITE

PS50887. GGDEF. 1 hit.
PS50110. RESPONSE_REGULATORY. 2 hits.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

B8GZM2.

Entry information

Entry name

PLED_CAUCN

Accession

Primary (citable) accession number: B8GZM2

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 10, 2010
Last sequence update:	March 3, 2009
Last modified:	May 1, 2013
This is version 37 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Including the following 1 domains:

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents