NUDK_ECOLI
ID NUDK_ECOLI Reviewed; 191 AA.
AC P37128; P77255;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=GDP-mannose pyrophosphatase {ECO:0000303|PubMed:16766526};
DE EC=3.6.1.- {ECO:0000269|PubMed:16766526, ECO:0000269|PubMed:21638333};
DE AltName: Full=GDP-mannose hydrolase {ECO:0000303|PubMed:21638333};
DE AltName: Full=GDPMK {ECO:0000303|PubMed:21638333};
GN Name=nudK;
GN Synonyms=yffH {ECO:0000303|PubMed:16766526, ECO:0000303|PubMed:21638333};
GN OrderedLocusNames=b2467, JW2451;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-157.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RA Cavicchioli R., Kolesnikow T., Gunsalus R.P.;
RL Submitted (JUN-1994) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16766526; DOI=10.1074/jbc.m603407200;
RA Xu W., Dunn C.A., O'Handley S.F., Smith D.L., Bessman M.J.;
RT "Three new Nudix hydrolases from Escherichia coli.";
RL J. Biol. Chem. 281:22794-22798(2006).
RN [6] {ECO:0007744|PDB:1VIU}
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 2-191, AND SUBUNIT.
RX PubMed=16021622; DOI=10.1002/prot.20541;
RA Badger J., Sauder J.M., Adams J.M., Antonysamy S., Bain K., Bergseid M.G.,
RA Buchanan S.G., Buchanan M.D., Batiyenko Y., Christopher J.A., Emtage S.,
RA Eroshkina A., Feil I., Furlong E.B., Gajiwala K.S., Gao X., He D.,
RA Hendle J., Huber A., Hoda K., Kearins P., Kissinger C., Laubert B.,
RA Lewis H.A., Lin J., Loomis K., Lorimer D., Louie G., Maletic M.,
RA Marsh C.D., Miller I., Molinari J., Muller-Dieckmann H.J., Newman J.M.,
RA Noland B.W., Pagarigan B., Park F., Peat T.S., Post K.W., Radojicic S.,
RA Ramos A., Romero R., Rutter M.E., Sanderson W.E., Schwinn K.D., Tresser J.,
RA Winhoven J., Wright T.A., Wu L., Xu J., Harris T.J.R.;
RT "Structural analysis of a set of proteins resulting from a bacterial
RT genomics project.";
RL Proteins 60:787-796(2005).
RN [7] {ECO:0007744|PDB:3O52, ECO:0007744|PDB:3O61, ECO:0007744|PDB:3O69, ECO:0007744|PDB:3O6Z}
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF WILD-TYPE AND MUTANTS ALA-100 AND
RP ALA-152 IN COMPLEXES WITH GDP-ALPHA-D-MANNOSE AND MAGNESIUM, FUNCTION,
RP CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE SPECIFICITY,
RP COFACTOR, SUBUNIT, DISRUPTION PHENOTYPE, DOMAIN, AND MUTAGENESIS OF ARG-44;
RP GLU-100; GLU-149; ASP-150; GLU-151; ASP-152 AND LYS-176.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21638333; DOI=10.1002/prot.23069;
RA Boto A.N., Xu W., Jakoncic J., Pannuri A., Romeo T., Bessman M.J.,
RA Gabelli S.B., Amzel L.M.;
RT "Structural studies of the Nudix GDP-mannose hydrolase from E. coli reveals
RT a new motif for mannose recognition.";
RL Proteins 79:2455-2466(2011).
CC -!- FUNCTION: Nucleoside diphosphate sugar hydrolase that hydrolyzes GDP-
CC mannose as its preferred substrate, yielding GMP and mannose-1-
CC phosphate. Can also hydrolyze the pyrophosphate bond of other sugar
CC nucleotides such as IDP-ribose, GDP-glucose, and to a lesser extent,
CC ADP-ribose, ADP-glucose and UDP-glucose. Shows no activity toward Nudix
CC substrates FAD, CDP-ethanolamine, CDP-choline, NAD(+), diadenosine
CC pentaphosphate, GTP, UTP, ATP, or CTP. {ECO:0000269|PubMed:16766526,
CC ECO:0000269|PubMed:21638333}.
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:0000269|PubMed:16766526, ECO:0000269|PubMed:21638333};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GDP-alpha-D-glucose + H2O = alpha-D-glucose 1-phosphate + GMP
CC + 2 H(+); Xref=Rhea:RHEA:62176, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:58115, ChEBI:CHEBI:58601, ChEBI:CHEBI:62230;
CC Evidence={ECO:0000269|PubMed:16766526, ECO:0000269|PubMed:21638333};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16766526, ECO:0000269|PubMed:21638333};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=659 uM for GDP-mannose (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:21638333};
CC KM=810 uM for GDP-mannose (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:16766526};
CC Vmax=207 umol/min/mg enzyme with GDP-mannose as substrate (at pH 8.5
CC and 37 degrees Celsius) {ECO:0000269|PubMed:16766526};
CC Note=kcat is 90.2 sec(-1) with GDP-mannose as substrate (at pH 8.5
CC and 37 degrees Celsius) (PubMed:21638333). The rate of hydrolysis of
CC GDP-glucose is half the rate of GDP-mannose (PubMed:21638333,
CC PubMed:16766526). {ECO:0000269|PubMed:16766526,
CC ECO:0000269|PubMed:21638333};
CC pH dependence:
CC Optimum pH is about 8.5. {ECO:0000269|PubMed:16766526,
CC ECO:0000269|PubMed:21638333};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16021622,
CC ECO:0000269|PubMed:21638333}.
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:0000269|PubMed:21638333}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show no defect in their
CC capacity of forming biofilms. {ECO:0000269|PubMed:21638333}.
CC -!- SIMILARITY: Belongs to the Nudix hydrolase family. NudK subfamily.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC75520.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16341.1; -; Genomic_DNA.
DR EMBL; L34011; AAB46945.1; -; Genomic_DNA.
DR PIR; B65022; B65022.
DR RefSeq; NP_416962.1; NC_000913.3.
DR RefSeq; WP_001300814.1; NZ_LN832404.1.
DR PDB; 1VIU; X-ray; 2.40 A; A/B/C/D=2-191.
DR PDB; 3O52; X-ray; 2.50 A; A/B/C/D/E=1-191.
DR PDB; 3O61; X-ray; 2.45 A; A/B/C/D=1-191.
DR PDB; 3O69; X-ray; 2.10 A; A/B=1-191.
DR PDB; 3O6Z; X-ray; 2.05 A; A/B=1-191.
DR PDBsum; 1VIU; -.
DR PDBsum; 3O52; -.
DR PDBsum; 3O61; -.
DR PDBsum; 3O69; -.
DR PDBsum; 3O6Z; -.
DR AlphaFoldDB; P37128; -.
DR SMR; P37128; -.
DR BioGRID; 4260924; 45.
DR IntAct; P37128; 10.
DR STRING; 511145.b2467; -.
DR jPOST; P37128; -.
DR PaxDb; P37128; -.
DR PRIDE; P37128; -.
DR EnsemblBacteria; AAC75520; AAC75520; b2467.
DR EnsemblBacteria; BAA16341; BAA16341; BAA16341.
DR GeneID; 947072; -.
DR KEGG; ecj:JW2451; -.
DR KEGG; eco:b2467; -.
DR PATRIC; fig|1411691.4.peg.4273; -.
DR EchoBASE; EB2309; -.
DR eggNOG; COG0494; Bacteria.
DR HOGENOM; CLU_062658_6_0_6; -.
DR InParanoid; P37128; -.
DR OMA; RTPAACI; -.
DR PhylomeDB; P37128; -.
DR BioCyc; EcoCyc:EG12410-MON; -.
DR BioCyc; MetaCyc:EG12410-MON; -.
DR EvolutionaryTrace; P37128; -.
DR PRO; PR:P37128; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0052751; F:GDP-mannose hydrolase activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0006753; P:nucleoside phosphate metabolic process; IBA:GO_Central.
DR GO; GO:0019693; P:ribose phosphate metabolic process; IBA:GO_Central.
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 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..191
FT /note="GDP-mannose pyrophosphatase"
FT /id="PRO_0000169231"
FT DOMAIN 43..180
FT /note="Nudix hydrolase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT MOTIF 79..106
FT /note="Nudix box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00794"
FT BINDING 17
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
FT BINDING 85
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O6Z"
FT BINDING 100
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O6Z"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O6Z"
FT BINDING 104
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O6Z"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
FT BINDING 151
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O6Z"
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:0000269|PubMed:21638333,
FT ECO:0007744|PDB:3O61"
FT MUTAGEN 44
FT /note="R->S: Decreases catalytic activity rate by a factor
FT of 53 and substrate affinity by at least 2-fold."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 100
FT /note="E->A: Abolishes Mg 2 binding. Abolishes catalytic
FT activity."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 149
FT /note="E->A: Does not affect catalytic activity rate and
FT substrate affinity."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 150
FT /note="D->A: Does not affect catalytic activity rate."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 151
FT /note="E->A: Decreases catalytic activity rate by a factor
FT of 4, but does not affect substrate affinity."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 152
FT /note="D->A: Decreases catalytic activity rate by a factor
FT of 2."
FT /evidence="ECO:0000269|PubMed:21638333"
FT MUTAGEN 176
FT /note="K->A: Decreases catalytic activity rate by a factor
FT of 820 and substrate affinity by at least 2-fold."
FT /evidence="ECO:0000269|PubMed:21638333"
FT STRAND 5..14
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 16..28
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 30..32
FT /evidence="ECO:0007829|PDB:1VIU"
FT STRAND 34..43
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 47..54
FT /evidence="ECO:0007829|PDB:3O6Z"
FT TURN 55..58
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 59..66
FT /evidence="ECO:0007829|PDB:3O6Z"
FT HELIX 68..71
FT /evidence="ECO:0007829|PDB:3O6Z"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 79..82
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 84..87
FT /evidence="ECO:0007829|PDB:3O6Z"
FT HELIX 93..104
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 112..120
FT /evidence="ECO:0007829|PDB:3O6Z"
FT TURN 122..124
FT /evidence="ECO:0007829|PDB:3O6Z"
FT STRAND 128..135
FT /evidence="ECO:0007829|PDB:3O6Z"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:3O61"
FT STRAND 152..159
FT /evidence="ECO:0007829|PDB:3O6Z"
FT HELIX 160..169
FT /evidence="ECO:0007829|PDB:3O6Z"
FT HELIX 175..187
FT /evidence="ECO:0007829|PDB:3O6Z"
FT TURN 188..190
FT /evidence="ECO:0007829|PDB:3O69"
SQ SEQUENCE 191 AA; 21749 MW; 13880625B41233C5 CRC64;
MTQQITLIKD KILSDNYFTL HNITYDLTRK DGEVIRHKRE VYDRGNGATI LLYNTKKKTV
VLIRQFRVAT WVNGNESGQL IESCAGLLDN DEPEVCIRKE AIEETGYEVG EVRKLFELYM
SPGGVTELIH FFIAEYSDNQ RANAGGGVED EDIEVLELPF SQALEMIKTG EIRDGKTVLL
LNYLQTSHLM D
