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Protein

Cyclic-di-AMP phosphodiesterase GdpP

Gene

gdpP

Organism
Geobacillus thermodenitrificans (strain NG80-2)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Has phosphodiesterase (PDE) activity against cyclic-di-AMP (c-di-AMP) and to a much lesser extent against cyclic-di-GMP (c-di-GMP) in the DHH/DHHA1 domains. Also has ATPase activity, probably via the GGDEF domain. May monitor cellular heme or NO levels.By similarity

Catalytic activityi

Cyclic di-3',5'-adenylate + H2O = 5'-phosphoadenylyl(3'->5')adenosine.

Cofactori

Protein has several cofactor binding sites:
  • heme b1 Publication1 PublicationNote: Binds 1 heme b per subunit.1 Publication
  • Mn2+By similarityNote: Probably binds 2 Mn2+ per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi346 – 3461Manganese 1By similarity
Metal bindingi350 – 3501Manganese 1By similarity
Metal bindingi352 – 3521Manganese 2By similarity
Metal bindingi421 – 4211Manganese 1By similarity
Metal bindingi421 – 4211Manganese 2By similarity
Metal bindingi445 – 4451Manganese 2By similarity
Metal bindingi500 – 5001Manganese 2By similarity

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Heme, Iron, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciGTHE420246:GIXT-3511-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Cyclic-di-AMP phosphodiesterase GdpP (EC:3.1.4.-)
Short name:
c-di-AMP phosphodiesterase
Gene namesi
Name:gdpP
Synonyms:yybT1 Publication
Ordered Locus Names:GTNG_3419
OrganismiGeobacillus thermodenitrificans (strain NG80-2)
Taxonomic identifieri420246 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeGeobacillus
Proteomesi
  • UP000001578 Componenti: Chromosome

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei12 – 3221HelicalSequence analysisAdd
BLAST
Transmembranei33 – 5321HelicalSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi107 – 1071F → A: Loss of heme b binding (by fragment with residues 55-162). 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 658658Cyclic-di-AMP phosphodiesterase GdpPPRO_0000436053Add
BLAST

Interactioni

Subunit structurei

The PAS-like domain (residues 55-162) dimerizes.1 Publication

Protein-protein interaction databases

STRINGi420246.GTNG_3419.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M1CNMR-A/B55-162[»]
ProteinModelPortaliA4ITV2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini174 – 302129GGDEFPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni83 – 16280PAS-like1 PublicationAdd
BLAST
Regioni340 – 497158DHHCuratedAdd
BLAST
Regioni590 – 64657DHHA1CuratedAdd
BLAST

Domaini

Binds heme b via the PAS-like domain.1 Publication

Sequence similaritiesi

Belongs to the GdpP/PdeA phosphodiesterase family.Curated
Contains 1 GGDEF domain.PROSITE-ProRule annotation

Keywords - Domaini

Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG4105BZR. Bacteria.
COG3887. LUCA.
HOGENOMiHOG000112075.
OMAiMPVGVIQ.
OrthoDBiEOG6FBX0G.

Family and domain databases

InterProiIPR001667. DDH_dom.
IPR003156. DHHA1_dom.
IPR000160. GGDEF_dom.
IPR014528. Signal_transd_YybT.
[Graphical view]
PfamiPF01368. DHH. 1 hit.
PF02272. DHHA1. 1 hit.
[Graphical view]
PIRSFiPIRSF026583. YybT. 1 hit.
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
PROSITEiPS50887. GGDEF. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

A4ITV2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSHFYERKTY RYPSYALAAL AVLMAVSLFY FQWMLGLVGL LGVGFLLYYV
60 70 80 90 100
IWSQRSLHKE LQQYISNLSY RVKKVSEEAL MQMPIGILLL DEEDKIEWSN
110 120 130 140 150
RFLAACFKEQ TLIGRSLAEL SEPLAAFVKK GKTDEEIIEL NGKQLKVIVH
160 170 180 190 200
RHERLLYFFD VTEHMELRRR YEIERLVLAI IFLDNYDEIT QGMDDQAKSQ
210 220 230 240 250
MNSLVTSVLN RWANDYGIFL KRTSSDRFIA VLNEHILTQL EKSKFSILDE
260 270 280 290 300
VREQTAKHQA QITLSIGIGA GVSSLPELGT LAQSSLDLAL GRGGDQVAIK
310 320 330 340 350
QGNGKVKFYG GKTNPMEKRT RVRARVISHA LRELIAESDK VLIMGHKYPD
360 370 380 390 400
MDALGAAIGI LKVVQSNQKE GFLVVDAMKT DAGAQRLLEE MKKQADLWAR
410 420 430 440 450
CIKPEQALEL ITEDTLLIVV DTHRPSLVIE ERLLYRADHI VVIDHHRRGE
460 470 480 490 500
EFIEAPILVY MEPYASSTSE LVTELLEYQP KRVKLSMLEA TALLAGIVVD
510 520 530 540 550
TKSFTLRTGS RTFDAASYLR AQGADTVLVQ KLLRESVANY VKRAKLIERA
560 570 580 590 600
AIDEHGIAIA KGDENEVHDQ VLIAQTADTL LTLSGVVASF VISKRGDGTV
610 620 630 640 650
GISARSLGDV NVQVIMERLG GGGHLTNAAA QLSDVTVGEA EQQLREAIHD

YFEGGKPV
Length:658
Mass (Da):73,706
Last modified:May 1, 2007 - v1
Checksum:iCD529279364A5D01
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000557 Genomic DNA. Translation: ABO68756.1.
RefSeqiWP_011888454.1. NC_009328.1.

Genome annotation databases

EnsemblBacteriaiABO68756; ABO68756; GTNG_3419.
KEGGigtn:GTNG_3419.
PATRICi21983503. VBIGeoThe136879_3594.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000557 Genomic DNA. Translation: ABO68756.1.
RefSeqiWP_011888454.1. NC_009328.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M1CNMR-A/B55-162[»]
ProteinModelPortaliA4ITV2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi420246.GTNG_3419.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABO68756; ABO68756; GTNG_3419.
KEGGigtn:GTNG_3419.
PATRICi21983503. VBIGeoThe136879_3594.

Phylogenomic databases

eggNOGiENOG4105BZR. Bacteria.
COG3887. LUCA.
HOGENOMiHOG000112075.
OMAiMPVGVIQ.
OrthoDBiEOG6FBX0G.

Enzyme and pathway databases

BioCyciGTHE420246:GIXT-3511-MONOMER.

Family and domain databases

InterProiIPR001667. DDH_dom.
IPR003156. DHHA1_dom.
IPR000160. GGDEF_dom.
IPR014528. Signal_transd_YybT.
[Graphical view]
PfamiPF01368. DHH. 1 hit.
PF02272. DHHA1. 1 hit.
[Graphical view]
PIRSFiPIRSF026583. YybT. 1 hit.
SMARTiSM00267. GGDEF. 1 hit.
[Graphical view]
PROSITEiPS50887. GGDEF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir."
    Feng L., Wang W., Cheng J., Ren Y., Zhao G., Gao C., Tang Y., Liu X., Han W., Peng X., Liu R., Wang L.
    Proc. Natl. Acad. Sci. U.S.A. 104:5602-5607(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: NG80-2.
  2. "Unusual heme-binding PAS domain from YybT family proteins."
    Rao F., Ji Q., Soehano I., Liang Z.X.
    J. Bacteriol. 193:1543-1551(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: COFACTOR, DOMAIN, MUTAGENESIS OF PHE-107.
  3. "Solution structure of the PAS domain of a thermophilic YybT protein homolog reveals a potential ligand-binding site."
    Tan E., Rao F., Pasunooti S., Pham T.H., Soehano I., Turner M.S., Liew C.W., Lescar J., Pervushin K., Liang Z.X.
    J. Biol. Chem. 288:11949-11959(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 55-162, POSSIBLE SUBUNIT.

Entry informationi

Entry nameiGDPP_GEOTN
AccessioniPrimary (citable) accession number: A4ITV2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 13, 2016
Last sequence update: May 1, 2007
Last modified: May 11, 2016
This is version 55 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.