ID A0A399D4Z8_9BACT Unreviewed; 507 AA.
AC A0A399D4Z8;
DT 05-DEC-2018, integrated into UniProtKB/TrEMBL.
DT 05-DEC-2018, sequence version 1.
DT 24-JAN-2024, entry version 20.
DE RecName: Full=Bifunctional NAD(P)H-hydrate repair enzyme {ECO:0000256|PIRNR:PIRNR017184};
DE AltName: Full=Nicotinamide nucleotide repair protein {ECO:0000256|PIRNR:PIRNR017184};
DE Includes:
DE RecName: Full=ADP-dependent (S)-NAD(P)H-hydrate dehydratase {ECO:0000256|PIRNR:PIRNR017184};
DE EC=4.2.1.136 {ECO:0000256|PIRNR:PIRNR017184};
DE AltName: Full=ADP-dependent NAD(P)HX dehydratase {ECO:0000256|PIRNR:PIRNR017184};
DE Includes:
DE RecName: Full=NAD(P)H-hydrate epimerase {ECO:0000256|PIRNR:PIRNR017184};
DE EC=5.1.99.6 {ECO:0000256|PIRNR:PIRNR017184};
GN Name=nnrD {ECO:0000256|HAMAP-Rule:MF_01965};
GN Synonyms=nnrE {ECO:0000256|HAMAP-Rule:MF_01966};
GN ORFNames=D1164_04985 {ECO:0000313|EMBL:RIH66268.1};
OS Mariniphaga sediminis.
OC Bacteria; Bacteroidota; Bacteroidia; Marinilabiliales; Prolixibacteraceae;
OC Mariniphaga.
OX NCBI_TaxID=1628158 {ECO:0000313|EMBL:RIH66268.1, ECO:0000313|Proteomes:UP000266441};
RN [1] {ECO:0000313|EMBL:RIH66268.1, ECO:0000313|Proteomes:UP000266441}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SY21 {ECO:0000313|EMBL:RIH66268.1,
RC ECO:0000313|Proteomes:UP000266441};
RX PubMed=26012581; DOI=10.1099/ijs.0.000354;
RA Wang F.Q., Shen Q.Y., Chen G.J., Du Z.J.;
RT "Mariniphaga sediminis sp. nov., isolated from coastal sediment.";
RL Int. J. Syst. Evol. Microbiol. 65:2908-2912(2015).
CC -!- FUNCTION: Bifunctional enzyme that catalyzes the epimerization of the
CC S- and R-forms of NAD(P)HX and the dehydration of the S-form of
CC NAD(P)HX at the expense of ADP, which is converted to AMP. This allows
CC the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that
CC is a result of enzymatic or heat-dependent hydration.
CC {ECO:0000256|ARBA:ARBA00025153, ECO:0000256|PIRNR:PIRNR017184}.
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:0000256|HAMAP-Rule:MF_01965}.
CC -!- FUNCTION: Catalyzes the epimerization of the S- and R-forms of
CC NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or
CC heat-dependent hydration. This is a prerequisite for the S-specific
CC NAD(P)H-hydrate dehydratase to allow the repair of both epimers of
CC NAD(P)HX. {ECO:0000256|HAMAP-Rule:MF_01966}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-NADHX = (6S)-NADHX; Xref=Rhea:RHEA:32215,
CC ChEBI:CHEBI:64074, ChEBI:CHEBI:64075; EC=5.1.99.6;
CC Evidence={ECO:0000256|ARBA:ARBA00000013, ECO:0000256|HAMAP-
CC Rule:MF_01966, ECO:0000256|PIRNR:PIRNR017184};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-NADPHX = (6S)-NADPHX; Xref=Rhea:RHEA:32227,
CC ChEBI:CHEBI:64076, ChEBI:CHEBI:64077; EC=5.1.99.6;
CC Evidence={ECO:0000256|ARBA:ARBA00000909, ECO:0000256|HAMAP-
CC Rule:MF_01966, ECO:0000256|PIRNR:PIRNR017184};
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;
CC Evidence={ECO:0000256|ARBA:ARBA00001026, ECO:0000256|HAMAP-
CC Rule:MF_01965, ECO:0000256|PIRNR:PIRNR017184};
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;
CC Evidence={ECO:0000256|ARBA:ARBA00001241, ECO:0000256|HAMAP-
CC Rule:MF_01965, ECO:0000256|PIRNR:PIRNR017184};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01966,
CC ECO:0000256|PIRNR:PIRNR017184};
CC Note=Binds 1 potassium ion per subunit. {ECO:0000256|HAMAP-
CC Rule:MF_01966, ECO:0000256|PIRNR:PIRNR017184};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01965};
CC -!- SUBUNIT: Homotetramer. {ECO:0000256|HAMAP-Rule:MF_01965}.
CC -!- SIMILARITY: Belongs to the NnrD/CARKD family. {ECO:0000256|HAMAP-
CC Rule:MF_01965}.
CC -!- SIMILARITY: Belongs to the NnrE/AIBP family. {ECO:0000256|HAMAP-
CC Rule:MF_01966}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the NnrD/CARKD
CC family. {ECO:0000256|ARBA:ARBA00009524, ECO:0000256|PIRNR:PIRNR017184}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the NnrE/AIBP family.
CC {ECO:0000256|ARBA:ARBA00006001, ECO:0000256|PIRNR:PIRNR017184}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_01966}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:RIH66268.1}.
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DR EMBL; QWET01000003; RIH66268.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A399D4Z8; -.
DR OrthoDB; 9806925at2; -.
DR Proteomes; UP000266441; Unassembled WGS sequence.
DR GO; GO:0052855; F:ADP-dependent NAD(P)H-hydrate dehydratase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0052856; F:NADHX epimerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0052857; F:NADPHX epimerase activity; IEA:UniProtKB-EC.
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 Gene3D; 3.40.50.10260; YjeF N-terminal domain; 1.
DR HAMAP; MF_01965; NADHX_dehydratase; 1.
DR HAMAP; MF_01966; NADHX_epimerase; 1.
DR InterPro; IPR017953; Carbohydrate_kinase_pred_CS.
DR InterPro; IPR000631; CARKD.
DR InterPro; IPR030677; Nnr.
DR InterPro; IPR029056; Ribokinase-like.
DR InterPro; IPR004443; YjeF_N_dom.
DR InterPro; IPR036652; YjeF_N_dom_sf.
DR NCBIfam; TIGR00196; yjeF_cterm; 1.
DR NCBIfam; TIGR00197; yjeF_nterm; 1.
DR PANTHER; PTHR12592:SF0; ATP-DEPENDENT (S)-NAD(P)H-HYDRATE DEHYDRATASE; 1.
DR PANTHER; PTHR12592; ATP-DEPENDENT (S)-NAD(P)H-HYDRATE DEHYDRATASE FAMILY MEMBER; 1.
DR Pfam; PF01256; Carb_kinase; 1.
DR Pfam; PF03853; YjeF_N; 1.
DR PIRSF; PIRSF017184; Nnr; 1.
DR SUPFAM; SSF53613; Ribokinase-like; 1.
DR SUPFAM; SSF64153; YjeF N-terminal domain-like; 1.
DR PROSITE; PS01050; YJEF_C_2; 1.
DR PROSITE; PS51383; YJEF_C_3; 1.
DR PROSITE; PS51385; YJEF_N; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01965};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01966};
KW Lyase {ECO:0000256|ARBA:ARBA00023239, ECO:0000256|HAMAP-Rule:MF_01965};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01966}; Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01965};
KW NADP {ECO:0000256|ARBA:ARBA00022857, ECO:0000256|HAMAP-Rule:MF_01965};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01965};
KW Potassium {ECO:0000256|HAMAP-Rule:MF_01966, ECO:0000256|PIRNR:PIRNR017184};
KW Reference proteome {ECO:0000313|Proteomes:UP000266441}.
FT DOMAIN 9..218
FT /note="YjeF N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51385"
FT DOMAIN 228..501
FT /note="YjeF C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51383"
FT BINDING 57..61
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 58
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 126
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 130..136
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 159
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 162
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 263
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 326
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 377
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 412..416
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 441
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 442
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
SQ SEQUENCE 507 AA; 55132 MW; 7824DA4F803D8C86 CRC64;
MKLFSTKQIA EVDRFTIENE PVTDIDLMER AAMQITTWID QRFSEENKMV FFAGPGNNGG
DALAVSRQLA ERGYRGAVYL LDFGKPLKGS PAINWKRLEE QGKVELHRIQ SIDDFPETNP
SDILIDGLFG SGLSRPLEGL PASIVRKING LPNKVIAIDI PSGLMGEDNS GNIPENIVNA
YFTLTLQFPK ISFLFSENER YTGSWEVLPI GLHPEGIAQT PSKLFLVDKK EVTGMIPRRS
RFAHKGTFGH ALLIAGSYGK MGASVLASKA CLRAGTGLLT SHVPRMGYSI IQTAVPEAMT
SVDPHDSIFT EFPDLSPFTA VGIGPGIGVK SNTRKALHEL LEKVQVPIVF DADALNILSE
NKEWLKQLPE NSILTPHPGE FRRLAGESVN TWERIQQQRQ MARELKVIIV LKGAFTTIAM
PDGKLFFNAT GNPGMATAGS GDTLTGIILG LLAQSLPPQH AAVVGVFLHG LAGDLAARKK
SINALIASDI TEFLGEAFLE MESVSAF
//
