NUDK_YERPP
ID NUDK_YERPP Reviewed; 198 AA.
AC A4TMK5;
DT 01-JUL-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 2.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=GDP-mannose pyrophosphatase;
DE EC=3.6.1.- {ECO:0000250|UniProtKB:P37128};
DE AltName: Full=GDP-mannose hydrolase;
DE AltName: Full=GDPMK;
GN Name=nudK; OrderedLocusNames=YPDSF_2140;
OS Yersinia pestis (strain Pestoides F).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=386656;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pestoides F;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Di Bartolo G., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J.,
RA Larimer F., Land M., Hauser L., Worsham P., Chu M., Bearden S., Garcia E.,
RA Richardson P.;
RT "Complete sequence of chromosome of Yersinia pestis Pestoides F.";
RL Submitted (FEB-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Nucleoside diphosphate sugar hydrolase that hydrolyzes GDP-
CC mannose as its preferred substrate, yielding GMP and mannose-1-
CC phosphate. {ECO:0000250|UniProtKB:P37128}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-mannose + H2O = alpha-D-mannose 1-phosphate + GMP
CC + 2 H(+); Xref=Rhea:RHEA:27978, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:57527, ChEBI:CHEBI:58115, ChEBI:CHEBI:58409;
CC Evidence={ECO:0000250|UniProtKB:P37128};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P37128};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P37128}.
CC -!- DOMAIN: In the dimer, the N-terminal domains are swapped between the
CC two monomers, such that residues of both chains contribute to the
CC active site. {ECO:0000250|UniProtKB:P37128}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudK subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=ABP40517.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000668; ABP40517.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_002208529.1; NZ_CP009715.1.
DR AlphaFoldDB; A4TMK5; -.
DR SMR; A4TMK5; -.
DR GeneID; 66844817; -.
DR KEGG; ypp:YPDSF_2140; -.
DR PATRIC; fig|386656.14.peg.3618; -.
DR GO; GO:0016818; F:hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR InterPro; IPR004385; NDP_pyrophosphatase.
DR InterPro; IPR015797; NUDIX_hydrolase-like_dom_sf.
DR InterPro; IPR000086; NUDIX_hydrolase_dom.
DR Pfam; PF00293; NUDIX; 1.
DR SUPFAM; SSF55811; SSF55811; 1.
DR TIGRFAMs; TIGR00052; TIGR00052; 1.
DR PROSITE; PS51462; NUDIX; 1.
PE 3: Inferred from homology;
KW Hydrolase; Magnesium; Metal-binding.
FT CHAIN 1..198
FT /note="GDP-mannose pyrophosphatase"
FT /id="PRO_0000342507"
FT DOMAIN 43..180
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 86..106
FT /note="Nudix box"
FT BINDING 38..40
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 67
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 85..87
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 85
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 100
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 104
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 127
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 150..151
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 151
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P37128"
FT BINDING 176
FT /ligand="GDP-alpha-D-mannose"
FT /ligand_id="ChEBI:CHEBI:57527"
FT /ligand_note="ligand shared between dimeric partners"
FT /note="in other chain"
FT /evidence="ECO:0000250|UniProtKB:P37128"
SQ SEQUENCE 198 AA; 22472 MW; 8CEB6975DAE1A14B CRC64;
MSVKIENIQC ELLSKNWFKL HKYTFDLKTD EGTSVQQIRE VYDRGNGATI LLYNRQQGTV
VLIEQFRMPT YVNGNASGML LEACAGLLDN DSPEACIRRE AMEETGYQVD KVQKLFEAYM
SPGGVTELVY FFAAEYHPDQ KITDEVGVED EVIEVVELPF HDALAMVADG RIKDGKTIML
LQYAQIHFFP SSLTPQRC
