GDPP_GEOTN
ID GDPP_GEOTN Reviewed; 658 AA.
AC A4ITV2;
DT 13-APR-2016, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=Cyclic-di-AMP phosphodiesterase GdpP;
DE Short=c-di-AMP phosphodiesterase;
DE EC=3.1.4.59 {ECO:0000250|UniProtKB:P37484};
GN Name=gdpP; Synonyms=yybT {ECO:0000303|PubMed:21257773};
GN OrderedLocusNames=GTNG_3419;
OS Geobacillus thermodenitrificans (strain NG80-2).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=420246;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NG80-2;
RX PubMed=17372208; DOI=10.1073/pnas.0609650104;
RA Feng L., Wang W., Cheng J., Ren Y., Zhao G., Gao C., Tang Y., Liu X.,
RA Han W., Peng X., Liu R., Wang L.;
RT "Genome and proteome of long-chain alkane degrading Geobacillus
RT thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:5602-5607(2007).
RN [2]
RP COFACTOR, DOMAIN, AND MUTAGENESIS OF PHE-107.
RX PubMed=21257773; DOI=10.1128/jb.01364-10;
RA Rao F., Ji Q., Soehano I., Liang Z.X.;
RT "Unusual heme-binding PAS domain from YybT family proteins.";
RL J. Bacteriol. 193:1543-1551(2011).
RN [3]
RP STRUCTURE BY NMR OF 55-162, AND POSSIBLE SUBUNIT.
RX PubMed=23504327; DOI=10.1074/jbc.m112.437764;
RA Tan E., Rao F., Pasunooti S., Pham T.H., Soehano I., Turner M.S.,
RA Liew C.W., Lescar J., Pervushin K., Liang Z.X.;
RT "Solution structure of the PAS domain of a thermophilic YybT protein
RT homolog reveals a potential ligand-binding site.";
RL J. Biol. Chem. 288:11949-11959(2013).
CC -!- FUNCTION: Has phosphodiesterase (PDE) activity against cyclic-di-AMP
CC (c-di-AMP) and to a much lesser extent against cyclic-di-GMP (c-di-GMP)
CC in the DHH/DHHA1 domains. Also has ATPase activity, probably via the
CC GGDEF domain. May monitor cellular heme or NO levels.
CC {ECO:0000250|UniProtKB:P37484}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3',3'-c-di-AMP + H2O = 5'-O-phosphonoadenylyl-(3'->5')-
CC adenosine + H(+); Xref=Rhea:RHEA:54420, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:71500, ChEBI:CHEBI:138171;
CC EC=3.1.4.59; Evidence={ECO:0000250|UniProtKB:P37484};
CC -!- COFACTOR:
CC Name=heme b; Xref=ChEBI:CHEBI:60344;
CC Evidence={ECO:0000269|PubMed:21257773, ECO:0000305|PubMed:23504327};
CC Note=Binds 1 heme b per subunit. {ECO:0000269|PubMed:21257773};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:P37484};
CC Note=Probably binds 2 Mn(2+) per subunit.
CC {ECO:0000250|UniProtKB:P37484};
CC -!- SUBUNIT: The PAS-like domain (residues 55-162) dimerizes.
CC {ECO:0000269|PubMed:23504327}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000255}; Multi-pass membrane
CC protein {ECO:0000255}.
CC -!- DOMAIN: Binds heme b via the PAS-like domain.
CC {ECO:0000269|PubMed:21257773}.
CC -!- SIMILARITY: Belongs to the GdpP/PdeA phosphodiesterase family.
CC {ECO:0000305}.
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DR EMBL; CP000557; ABO68756.1; -; Genomic_DNA.
DR RefSeq; WP_011888454.1; NC_009328.1.
DR PDB; 2M1C; NMR; -; A/B=55-162.
DR PDBsum; 2M1C; -.
DR AlphaFoldDB; A4ITV2; -.
DR SMR; A4ITV2; -.
DR STRING; 420246.GTNG_3419; -.
DR EnsemblBacteria; ABO68756; ABO68756; GTNG_3419.
DR KEGG; gtn:GTNG_3419; -.
DR eggNOG; COG3887; Bacteria.
DR HOGENOM; CLU_018278_0_0_9; -.
DR OMA; STCELVT; -.
DR OrthoDB; 128306at2; -.
DR BRENDA; 3.1.4.59; 705.
DR Proteomes; UP000001578; Chromosome.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0106409; F:cyclic-di-AMP phosphodiesterase activity; IEA:UniProtKB-EC.
DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003676; F:nucleic acid binding; IEA:InterPro.
DR InterPro; IPR001667; DDH_dom.
DR InterPro; IPR038763; DHH_sf.
DR InterPro; IPR003156; DHHA1_dom.
DR InterPro; IPR014528; GdpP/PdeA.
DR InterPro; IPR000160; GGDEF_dom.
DR Pfam; PF01368; DHH; 1.
DR Pfam; PF02272; DHHA1; 1.
DR PIRSF; PIRSF026583; YybT; 1.
DR SMART; SM00267; GGDEF; 1.
DR SUPFAM; SSF64182; SSF64182; 1.
DR PROSITE; PS50887; GGDEF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell membrane; Heme; Hydrolase; Iron; Manganese; Membrane;
KW Metal-binding; Transmembrane; Transmembrane helix.
FT CHAIN 1..658
FT /note="Cyclic-di-AMP phosphodiesterase GdpP"
FT /id="PRO_0000436053"
FT TRANSMEM 12..32
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TRANSMEM 33..53
FT /note="Helical"
FT /evidence="ECO:0000255"
FT DOMAIN 174..302
FT /note="GGDEF"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00095"
FT REGION 83..162
FT /note="PAS-like"
FT /evidence="ECO:0000303|PubMed:21257773"
FT REGION 340..497
FT /note="DHH"
FT /evidence="ECO:0000305"
FT REGION 590..646
FT /note="DHHA1"
FT /evidence="ECO:0000305"
FT BINDING 346
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 350
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 352
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 421
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 421
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 445
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT BINDING 500
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37484"
FT MUTAGEN 107
FT /note="F->A: Loss of heme b binding (by fragment with
FT residues 55-162)."
FT /evidence="ECO:0000269|PubMed:21257773"
FT HELIX 59..64
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 65..68
FT /evidence="ECO:0007829|PDB:2M1C"
FT TURN 74..78
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 80..83
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 87..90
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 96..99
FT /evidence="ECO:0007829|PDB:2M1C"
FT HELIX 102..105
FT /evidence="ECO:0007829|PDB:2M1C"
FT TURN 106..108
FT /evidence="ECO:0007829|PDB:2M1C"
FT TURN 116..120
FT /evidence="ECO:0007829|PDB:2M1C"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:2M1C"
FT TURN 128..130
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 133..140
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 143..148
FT /evidence="ECO:0007829|PDB:2M1C"
FT STRAND 157..161
FT /evidence="ECO:0007829|PDB:2M1C"
SQ SEQUENCE 658 AA; 73706 MW; CD529279364A5D01 CRC64;
MSHFYERKTY RYPSYALAAL AVLMAVSLFY FQWMLGLVGL LGVGFLLYYV IWSQRSLHKE
LQQYISNLSY RVKKVSEEAL MQMPIGILLL DEEDKIEWSN RFLAACFKEQ TLIGRSLAEL
SEPLAAFVKK GKTDEEIIEL NGKQLKVIVH RHERLLYFFD VTEHMELRRR YEIERLVLAI
IFLDNYDEIT QGMDDQAKSQ MNSLVTSVLN RWANDYGIFL KRTSSDRFIA VLNEHILTQL
EKSKFSILDE VREQTAKHQA QITLSIGIGA GVSSLPELGT LAQSSLDLAL GRGGDQVAIK
QGNGKVKFYG GKTNPMEKRT RVRARVISHA LRELIAESDK VLIMGHKYPD MDALGAAIGI
LKVVQSNQKE GFLVVDAMKT DAGAQRLLEE MKKQADLWAR CIKPEQALEL ITEDTLLIVV
DTHRPSLVIE ERLLYRADHI VVIDHHRRGE EFIEAPILVY MEPYASSTSE LVTELLEYQP
KRVKLSMLEA TALLAGIVVD TKSFTLRTGS RTFDAASYLR AQGADTVLVQ KLLRESVANY
VKRAKLIERA AIDEHGIAIA KGDENEVHDQ VLIAQTADTL LTLSGVVASF VISKRGDGTV
GISARSLGDV NVQVIMERLG GGGHLTNAAA QLSDVTVGEA EQQLREAIHD YFEGGKPV
