ID Q2Y6E8_NITMU Unreviewed; 522 AA.
AC Q2Y6E8;
DT 20-DEC-2005, integrated into UniProtKB/TrEMBL.
DT 20-DEC-2005, sequence version 1.
DT 27-MAR-2024, entry version 108.
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=nnrE {ECO:0000256|HAMAP-Rule:MF_01966};
GN Synonyms=nnrD {ECO:0000256|HAMAP-Rule:MF_01965};
GN OrderedLocusNames=Nmul_A2384 {ECO:0000313|EMBL:ABB75673.1};
GN ORFNames=SAMN05216403_11636 {ECO:0000313|EMBL:SEF93469.1};
OS Nitrosospira multiformis (strain ATCC 25196 / NCIMB 11849 / C 71).
OC Bacteria; Pseudomonadota; Betaproteobacteria; Nitrosomonadales;
OC Nitrosomonadaceae; Nitrosospira.
OX NCBI_TaxID=323848 {ECO:0000313|EMBL:ABB75673.1, ECO:0000313|Proteomes:UP000002718};
RN [1] {ECO:0000313|EMBL:ABB75673.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB75673.1};
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of Chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 / NCIMB 11849 / C 71
RC {ECO:0000313|Proteomes:UP000002718};
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Lykidis A., Richardson P.;
RT "Complete sequence of chromosome 1 of Nitrosospira multiformis ATCC
RT 25196.";
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|EMBL:ABB75673.1, ECO:0000313|Proteomes:UP000002718}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25196 {ECO:0000313|EMBL:ABB75673.1}, and ATCC 25196 /
RC NCIMB 11849 / C 71 {ECO:0000313|Proteomes:UP000002718};
RX PubMed=18390676; DOI=10.1128/AEM.02722-07;
RA Norton J.M., Klotz M.G., Stein L.Y., Arp D.J., Bottomley P.J., Chain P.S.,
RA Hauser L.J., Land M.L., Larimer F.W., Shin M.W., Starkenburg S.R.;
RT "Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing
RT bacterium from the soil environment.";
RL Appl. Environ. Microbiol. 74:3559-3572(2008).
RN [4] {ECO:0000313|EMBL:SEF93469.1, ECO:0000313|Proteomes:UP000236751}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Nl13 {ECO:0000313|EMBL:SEF93469.1,
RC ECO:0000313|Proteomes:UP000236751};
RA de Groot N.N.;
RL Submitted (OCT-2016) to the EMBL/GenBank/DDBJ databases.
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}.
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DR EMBL; CP000103; ABB75673.1; -; Genomic_DNA.
DR EMBL; FNVK01000016; SEF93469.1; -; Genomic_DNA.
DR RefSeq; WP_011381674.1; NZ_FNVK01000016.1.
DR AlphaFoldDB; Q2Y6E8; -.
DR STRING; 323848.Nmul_A2384; -.
DR KEGG; nmu:Nmul_A2384; -.
DR eggNOG; COG0062; Bacteria.
DR eggNOG; COG0063; Bacteria.
DR HOGENOM; CLU_024853_4_3_4; -.
DR OrthoDB; 9806925at2; -.
DR Proteomes; UP000002718; Chromosome.
DR Proteomes; UP000236751; 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:0016301; F:kinase activity; IEA:UniProtKB-KW.
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 GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
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; 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; 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 Kinase {ECO:0000313|EMBL:SEF93469.1};
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:UP000002718};
KW Transferase {ECO:0000313|EMBL:SEF93469.1}.
FT DOMAIN 13..223
FT /note="YjeF N-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51385"
FT DOMAIN 232..508
FT /note="YjeF C-terminal"
FT /evidence="ECO:0000259|PROSITE:PS51383"
FT BINDING 66..70
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 67
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 129
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 148
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 166
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 169
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01966"
FT BINDING 267
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 324
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 381
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 418..422
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 447
FT /ligand="AMP"
FT /ligand_id="ChEBI:CHEBI:456215"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
FT BINDING 448
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01965"
SQ SEQUENCE 522 AA; 54889 MW; 5C834494FCADAF40 CRC64;
MNALKNNLST AIYSTAEIRE IEHLAAGLPG RPQLMEAAGL AAAEIARDRL LSPHKPRLLV
LAGPGNNGGD AFVAARHLRE WGFKVTLVFT GEQAKLSADA LRALNAWVAT GAGMVSEIPE
NETWDAVIDG LFGIGLDQQG GRELGGKYLA MVNTVNAMML PVLSIDIPSG LGSDTGAVCG
AAIIATMTAT FIGLKPGLFT NEGPDYCGKV FLHDLDLDVS SLKKPDAWLM DQMHIRRLLP
PPRRANSHKG MFGSIGVIGG TAGMVGAALL AGTAALKLGA GRVYLGLMAP DAPAVDTFQP
ELMLRPIQDL FKLEQLNCLV VGPGLGTETA AYFWLKCALQ TTLPLVLDAD GLNLVASHSE
IAGLLRERLR ERHAPSILTP HPAEAARLLK STTTSVQQDR MAAAAELAQR FNCWIVLKGA
GSVCAMPEGR RFINTSGNPG LSSAGTGDIL SGMIGAFLAQ RSSPENALLA AVYLHGAAAD
VLQKQYGGGI GMTASEIPNV ARNLLNQWIA VNSAPAPHQQ EG
//