NNRD_BACSU
ID NNRD_BACSU Reviewed; 276 AA.
AC P94368;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=ADP-dependent (S)-NAD(P)H-hydrate dehydratase {ECO:0000255|HAMAP-Rule:MF_01965};
DE EC=4.2.1.136 {ECO:0000255|HAMAP-Rule:MF_01965};
DE AltName: Full=ADP-dependent NAD(P)HX dehydratase {ECO:0000255|HAMAP-Rule:MF_01965};
GN Name=nnrD {ECO:0000255|HAMAP-Rule:MF_01965}; Synonyms=yxkO;
GN OrderedLocusNames=BSU38720;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / BGSC1A1;
RX PubMed=8969509; DOI=10.1099/13500872-142-11-3113;
RA Yoshida K., Shindo K., Sano H., Seki S., Fujimura M., Yanai N., Miwa Y.,
RA Fujita Y.;
RT "Sequencing of a 65 kb region of the Bacillus subtilis genome containing
RT the lic and cel loci, and creation of a 177 kb contig covering the gnt-
RT sacXY region.";
RL Microbiology 142:3113-3123(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3] {ECO:0007744|PDB:1KYH}
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND SUBUNIT.
RX PubMed=12457846; DOI=10.1016/s1047-8477(02)00532-4;
RA Zhang R.G., Grembecka J., Vinokour E., Collart F., Dementieva I., Minor W.,
RA Joachimiak A.;
RT "Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a
RT putative kinase.";
RL J. Struct. Biol. 139:161-170(2002).
RN [4] {ECO:0007744|PDB:3RPH, ECO:0007744|PDB:3RPZ, ECO:0007744|PDB:3RQ2, ECO:0007744|PDB:3RQ5, ECO:0007744|PDB:3RQ6, ECO:0007744|PDB:3RQ8, ECO:0007744|PDB:3RQH, ECO:0007744|PDB:3RQQ, ECO:0007744|PDB:3RQX}
RP X-RAY CRYSTALLOGRAPHY (1.51 ANGSTROMS) IN COMPLEXES WITH AMP; NAD; NADPHX
RP AND MAGNESIUM, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=22940582; DOI=10.1016/j.str.2012.07.016;
RA Shumilin I.A., Cymborowski M., Chertihin O., Jha K.N., Herr J.C.,
RA Lesley S.A., Joachimiak A., Minor W.;
RT "Identification of unknown protein function using metabolite cocktail
RT screening.";
RL Structure 20:1715-1725(2012).
CC -!- FUNCTION: Catalyzes the dehydration of the S-form of NAD(P)HX at the
CC expense of ADP, which is converted to AMP. Together with NAD(P)HX
CC epimerase, which catalyzes the epimerization of the S- and R-forms, the
CC enzyme allows the repair of both epimers of NAD(P)HX, a damaged form of
CC NAD(P)H that is a result of enzymatic or heat-dependent hydration.
CC {ECO:0000255|HAMAP-Rule:MF_01965, ECO:0000269|PubMed:22940582}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-NADHX + ADP = AMP + H(+) + NADH + phosphate;
CC Xref=Rhea:RHEA:32223, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:64074, ChEBI:CHEBI:456215,
CC ChEBI:CHEBI:456216; EC=4.2.1.136; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01965, ECO:0000269|PubMed:22940582};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32224;
CC Evidence={ECO:0000305|PubMed:22940582};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-NADPHX + ADP = AMP + H(+) + NADPH + phosphate;
CC Xref=Rhea:RHEA:32235, ChEBI:CHEBI:15378, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:57783, ChEBI:CHEBI:64076, ChEBI:CHEBI:456215,
CC ChEBI:CHEBI:456216; EC=4.2.1.136; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01965, ECO:0000269|PubMed:22940582};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:32236;
CC Evidence={ECO:0000305|PubMed:22940582};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01965,
CC ECO:0000269|PubMed:22940582};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.30 uM for NADHX {ECO:0000269|PubMed:22940582};
CC KM=6.43 uM for ADP {ECO:0000269|PubMed:22940582};
CC Note=kcat is 0.35 sec(-1) for the ADP-dependent dehydration of NADHX.
CC {ECO:0000269|PubMed:22940582};
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_01965,
CC ECO:0000269|PubMed:12457846, ECO:0000269|PubMed:22940582}.
CC -!- SIMILARITY: Belongs to the NnrD/CARKD family. {ECO:0000255|HAMAP-
CC Rule:MF_01965}.
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DR EMBL; D83026; BAA11731.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB15898.1; -; Genomic_DNA.
DR PIR; D70081; D70081.
DR RefSeq; NP_391751.1; NC_000964.3.
DR RefSeq; WP_003244033.1; NZ_JNCM01000034.1.
DR PDB; 1KYH; X-ray; 1.60 A; A=1-276.
DR PDB; 3RPH; X-ray; 1.75 A; A=1-276.
DR PDB; 3RPZ; X-ray; 1.51 A; A=1-276.
DR PDB; 3RQ2; X-ray; 1.80 A; A=1-276.
DR PDB; 3RQ5; X-ray; 1.70 A; A=1-276.
DR PDB; 3RQ6; X-ray; 1.65 A; A=1-276.
DR PDB; 3RQ8; X-ray; 1.90 A; A=1-276.
DR PDB; 3RQH; X-ray; 1.75 A; A=1-276.
DR PDB; 3RQQ; X-ray; 1.60 A; A=1-276.
DR PDB; 3RQX; X-ray; 1.60 A; A=1-276.
DR PDBsum; 1KYH; -.
DR PDBsum; 3RPH; -.
DR PDBsum; 3RPZ; -.
DR PDBsum; 3RQ2; -.
DR PDBsum; 3RQ5; -.
DR PDBsum; 3RQ6; -.
DR PDBsum; 3RQ8; -.
DR PDBsum; 3RQH; -.
DR PDBsum; 3RQQ; -.
DR PDBsum; 3RQX; -.
DR AlphaFoldDB; P94368; -.
DR SMR; P94368; -.
DR DIP; DIP-59951N; -.
DR STRING; 224308.BSU38720; -.
DR PaxDb; P94368; -.
DR PRIDE; P94368; -.
DR DNASU; 937408; -.
DR EnsemblBacteria; CAB15898; CAB15898; BSU_38720.
DR GeneID; 937408; -.
DR KEGG; bsu:BSU38720; -.
DR PATRIC; fig|224308.179.peg.4191; -.
DR eggNOG; COG0063; Bacteria.
DR InParanoid; P94368; -.
DR OMA; ATYWRDG; -.
DR PhylomeDB; P94368; -.
DR BioCyc; BSUB:BSU38720-MON; -.
DR BRENDA; 4.2.1.136; 658.
DR BRENDA; 4.2.1.93; 658.
DR EvolutionaryTrace; P94368; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0052855; F:ADP-dependent NAD(P)H-hydrate dehydratase activity; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0052856; F:NADHX epimerase activity; IBA:GO_Central.
DR GO; GO:0052857; F:NADPHX epimerase activity; IBA:GO_Central.
DR GO; GO:0110051; P:metabolite repair; IBA:GO_Central.
DR GO; GO:0046496; P:nicotinamide nucleotide metabolic process; IEA:UniProtKB-UniRule.
DR CDD; cd01171; YXKO-related; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_01965; NADHX_dehydratase; 1.
DR InterPro; IPR017953; Carbohydrate_kinase_pred_CS.
DR InterPro; IPR000631; CARKD.
DR InterPro; IPR029056; Ribokinase-like.
DR Pfam; PF01256; Carb_kinase; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR00196; yjeF_cterm; 1.
DR PROSITE; PS01049; YJEF_C_1; 1.
DR PROSITE; PS01050; YJEF_C_2; 1.
DR PROSITE; PS51383; YJEF_C_3; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Lyase; NAD; NADP; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..276
FT /note="ADP-dependent (S)-NAD(P)H-hydrate dehydratase"
FT /id="PRO_0000119046"
FT DOMAIN 7..275
FT /note="YjeF C-terminal"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01965"
FT BINDING 42
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT BINDING 104
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT BINDING 149
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT BINDING 186..190
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT BINDING 215
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT BINDING 216
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000269|PubMed:22940582,
FT ECO:0007744|PDB:3RPZ"
FT HELIX 8..14
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 24..27
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 29..33
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 37..39
FT /evidence="ECO:0007829|PDB:3RQQ"
FT HELIX 41..51
FT /evidence="ECO:0007829|PDB:3RPZ"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:3RPZ"
FT TURN 64..66
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 67..70
FT /evidence="ECO:0007829|PDB:3RPZ"
FT TURN 71..73
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 83..86
FT /evidence="ECO:0007829|PDB:3RPZ"
FT TURN 87..89
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 109..118
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 129..131
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 150..157
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 161..164
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 168..179
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:3RQ8"
FT STRAND 191..193
FT /evidence="ECO:0007829|PDB:3RPZ"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 214..228
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 232..253
FT /evidence="ECO:0007829|PDB:3RPZ"
FT HELIX 256..258
FT /evidence="ECO:0007829|PDB:1KYH"
FT HELIX 261..274
FT /evidence="ECO:0007829|PDB:3RPZ"
SQ SEQUENCE 276 AA; 29870 MW; 68C14E747419478A CRC64;
MNVPFWTEEH VRATLPERDA ESHKGTYGTA LLLAGSDDMP GAALLAGLGA MRSGLGKLVI
GTSENVIPLI VPVLPEATYW RDGWKKAADA QLEETYRAIA IGPGLPQTES VQQAVDHVLT
ADCPVILDAG ALAKRTYPKR EGPVILTPHP GEFFRMTGVP VNELQKKRAE YAKEWAAQLQ
TVIVLKGNQT VIAFPDGDCW LNPTGNGALA KGGTGDTLTG MILGMLCCHE DPKHAVLNAV
YLHGACAELW TDEHSAHTLL AHELSDILPR VWKRFE
