NADE_PYRHO
ID NADE_PYRHO Reviewed; 257 AA.
AC O57921;
DT 15-JUL-1999, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=NH(3)-dependent NAD(+) synthetase {ECO:0000255|HAMAP-Rule:MF_00193};
DE EC=6.3.1.5 {ECO:0000255|HAMAP-Rule:MF_00193};
GN Name=nadE {ECO:0000255|HAMAP-Rule:MF_00193}; OrderedLocusNames=PH0182;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
RN [2] {ECO:0007744|PDB:2E18}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS).
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RA Shimizu K., Kunishima N.;
RT "Crystal structure of project PH0182 from Pyrococcus horikoshii OT3.";
RL Submitted (OCT-2006) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the ATP-dependent amidation of deamido-NAD to form
CC NAD. Uses ammonia as a nitrogen source. {ECO:0000255|HAMAP-
CC Rule:MF_00193}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + deamido-NAD(+) + NH4(+) = AMP + diphosphate + H(+) +
CC NAD(+); Xref=Rhea:RHEA:21188, ChEBI:CHEBI:15378, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:58437, ChEBI:CHEBI:456215; EC=6.3.1.5;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00193};
CC -!- PATHWAY: Cofactor biosynthesis; NAD(+) biosynthesis; NAD(+) from
CC deamido-NAD(+) (ammonia route): step 1/1. {ECO:0000255|HAMAP-
CC Rule:MF_00193}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00193}.
CC -!- SIMILARITY: Belongs to the NAD synthetase family. {ECO:0000255|HAMAP-
CC Rule:MF_00193, ECO:0000305}.
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DR EMBL; BA000001; BAA29251.1; -; Genomic_DNA.
DR PIR; D71240; D71240.
DR RefSeq; WP_010884291.1; NC_000961.1.
DR PDB; 2E18; X-ray; 2.10 A; A/B=1-257.
DR PDBsum; 2E18; -.
DR AlphaFoldDB; O57921; -.
DR SMR; O57921; -.
DR STRING; 70601.3256568; -.
DR EnsemblBacteria; BAA29251; BAA29251; BAA29251.
DR GeneID; 1444073; -.
DR KEGG; pho:PH0182; -.
DR eggNOG; arCOG00069; Archaea.
DR OMA; MAFLYDY; -.
DR OrthoDB; 89944at2157; -.
DR UniPathway; UPA00253; UER00333.
DR EvolutionaryTrace; O57921; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003690; F:double-stranded DNA binding; IEA:InterPro.
DR GO; GO:0004359; F:glutaminase activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003952; F:NAD+ synthase (glutamine-hydrolyzing) activity; IEA:InterPro.
DR GO; GO:0008795; F:NAD+ synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR GO; GO:0009435; P:NAD biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd00553; NAD_synthase; 1.
DR Gene3D; 3.40.50.620; -; 1.
DR HAMAP; MF_00193; NadE_ammonia_dep; 1.
DR InterPro; IPR022310; NAD/GMP_synthase.
DR InterPro; IPR003694; NAD_synthase.
DR InterPro; IPR022926; NH(3)-dep_NAD(+)_synth.
DR InterPro; IPR014729; Rossmann-like_a/b/a_fold.
DR InterPro; IPR018126; SASP_alpha/beta-type_CS.
DR PANTHER; PTHR23090; PTHR23090; 1.
DR Pfam; PF02540; NAD_synthase; 1.
DR TIGRFAMs; TIGR00552; nadE; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Magnesium; Metal-binding; NAD;
KW Nucleotide-binding.
FT CHAIN 1..257
FT /note="NH(3)-dependent NAD(+) synthetase"
FT /id="PRO_0000152232"
FT BINDING 28..35
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 34
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 109
FT /ligand="deamido-NAD(+)"
FT /ligand_id="ChEBI:CHEBI:58437"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 134
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 142
FT /ligand="deamido-NAD(+)"
FT /ligand_id="ChEBI:CHEBI:58437"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 149
FT /ligand="deamido-NAD(+)"
FT /ligand_id="ChEBI:CHEBI:58437"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 158
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 180
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT BINDING 240..241
FT /ligand="deamido-NAD(+)"
FT /ligand_id="ChEBI:CHEBI:58437"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00193"
FT HELIX 6..20
FT /evidence="ECO:0007829|PDB:2E18"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 33..46
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 48..50
FT /evidence="ECO:0007829|PDB:2E18"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 63..74
FT /evidence="ECO:0007829|PDB:2E18"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 84..94
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 100..122
FT /evidence="ECO:0007829|PDB:2E18"
FT STRAND 125..127
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 132..137
FT /evidence="ECO:0007829|PDB:2E18"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:2E18"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 158..168
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 172..176
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 189..193
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 197..208
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 214..219
FT /evidence="ECO:0007829|PDB:2E18"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 225..236
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 237..241
FT /evidence="ECO:0007829|PDB:2E18"
FT HELIX 251..253
FT /evidence="ECO:0007829|PDB:2E18"
SQ SEQUENCE 257 AA; 28862 MW; 86A9CF2CC6F387FC CRC64;
MRILDYDKVI ERILEFIREK GNNGVVIGIS GGVDSATVAY LATKALGKEK VLGLIMPYFE
NKDVEDAKLV AEKLGIGYKV INIKPIVDSF VENLELNLDR KGLGNIMSRT RMIMLYAHAN
SLGRIVLGTS NRSEFLTGYF TKWGDGASDY APIINLYKTE VWEIAKRIGV PERIVKKKPS
AGLWEGQTDE DELGISYNLL DEILWRMIDL KIGKEEIAKD LGIPLSLVER VEELIKKSEH
KRRLPIGPSF EDLIVGP
