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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)DescriptionActionsGraphical viewLength
Metal bindingi346Manganese 1By similarity1
Metal bindingi350Manganese 1By similarity1
Metal bindingi352Manganese 2By similarity1
Metal bindingi421Manganese 1By similarity1
Metal bindingi421Manganese 2By similarity1
Metal bindingi445Manganese 2By similarity1
Metal bindingi500Manganese 2By similarity1

GO - Molecular functioni

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Heme, Iron, Manganese, Metal-binding

Enzyme and pathway databases

BioCyciGTHE420246:GIXT-3487-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)DescriptionActionsGraphical viewLength
Transmembranei12 – 32HelicalSequence analysisAdd BLAST21
Transmembranei33 – 53HelicalSequence analysisAdd BLAST21

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi107F → A: Loss of heme b binding (by fragment with residues 55-162). 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004360531 – 658Cyclic-di-AMP phosphodiesterase GdpPAdd BLAST658

Interactioni

Subunit structurei

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

Protein-protein interaction databases

STRINGi420246.GTNG_3419.

Structurei

Secondary structure

1658
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi59 – 64Combined sources6
Beta strandi65 – 68Combined sources4
Turni74 – 78Combined sources5
Beta strandi80 – 83Combined sources4
Beta strandi87 – 90Combined sources4
Beta strandi92 – 94Combined sources3
Beta strandi96 – 99Combined sources4
Helixi102 – 105Combined sources4
Turni106 – 108Combined sources3
Turni116 – 120Combined sources5
Helixi123 – 127Combined sources5
Turni128 – 130Combined sources3
Beta strandi133 – 140Combined sources8
Beta strandi143 – 148Combined sources6
Beta strandi157 – 161Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M1CNMR-A/B55-162[»]
ProteinModelPortaliA4ITV2.
SMRiA4ITV2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini174 – 302GGDEFPROSITE-ProRule annotationAdd BLAST129

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni83 – 162PAS-like1 PublicationAdd BLAST80
Regioni340 – 497DHHCuratedAdd BLAST158
Regioni590 – 646DHHA1CuratedAdd BLAST57

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.
OrthoDBiPOG091H01MJ.

Family and domain databases

InterProiIPR001667. DDH_dom.
IPR003156. DHHA1_dom.
IPR014528. GdpP/PdeA.
IPR000160. GGDEF_dom.
[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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M1CNMR-A/B55-162[»]
ProteinModelPortaliA4ITV2.
SMRiA4ITV2.
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.
OrthoDBiPOG091H01MJ.

Enzyme and pathway databases

BioCyciGTHE420246:GIXT-3487-MONOMER.

Family and domain databases

InterProiIPR001667. DDH_dom.
IPR003156. DHHA1_dom.
IPR014528. GdpP/PdeA.
IPR000160. GGDEF_dom.
[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...

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: 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. 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.