RIB7_METJA
ID RIB7_METJA Reviewed; 224 AA.
AC Q58085;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase;
DE Short=DAROPP reductase;
DE Short=DARP reductase;
DE EC=1.1.1.302;
DE AltName: Full=2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one reductase;
DE AltName: Full=2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthase;
DE Short=DARIPP synthase;
DE AltName: Full=MjaRED;
GN Name=arfC; OrderedLocusNames=MJ0671;
OS Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS 10045 / NBRC 100440) (Methanococcus jannaschii).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanocaldococcaceae; Methanocaldococcus.
OX NCBI_TaxID=243232;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT jannaschii.";
RL Science 273:1058-1073(1996).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBSTRATE SPECIFICITY.
RX PubMed=11889103; DOI=10.1128/jb.184.7.1952-1957.2002;
RA Graupner M., Xu H., White R.H.;
RT "The pyrimidine nucleotide reductase step in riboflavin and F(420)
RT biosynthesis in archaea proceeds by the eukaryotic route to riboflavin.";
RL J. Bacteriol. 184:1952-1957(2002).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, AND REACTION STEREOSPECIFICITY.
RX PubMed=18671734; DOI=10.1111/j.1742-4658.2008.06586.x;
RA Romisch-Margl W., Eisenreich W., Haase I., Bacher A., Fischer M.;
RT "2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate synthases of
RT fungi and archaea.";
RL FEBS J. 275:4403-4414(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 6-224 IN COMPLEX WITH NADP,
RP PROTEIN SEQUENCE OF 2-11, CATALYTIC ACTIVITY, MASS SPECTROMETRY, SUBUNIT,
RP AND REACTION MECHANISM.
RX PubMed=16730025; DOI=10.1016/j.jmb.2006.04.045;
RA Chatwell L., Krojer T., Fidler A., Romisch W., Eisenreich W., Bacher A.,
RA Huber R., Fischer M.;
RT "Biosynthesis of riboflavin: structure and properties of 2,5-diamino-6-
RT ribosylamino-4(3H)-pyrimidinone 5'-phosphate reductase of
RT Methanocaldococcus jannaschii.";
RL J. Mol. Biol. 359:1334-1351(2006).
CC -!- FUNCTION: Catalyzes an early step in riboflavin biosynthesis, the
CC NAD(P)H-dependent reduction of the ribose side chain of 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate, yielding 2,5-diamino-6-
CC ribitylamino-4(3H)-pyrimidinone 5'-phosphate. The beta anomer is the
CC authentic substrate, and the alpha anomer can serve as substrate
CC subsequent to spontaneous anomerization. NADPH and NADH function
CC equally well as the reductants. Does not catalyze the reduction of 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil to 5-amino-6-(5-phospho-D-
CC ribitylamino)uracil. {ECO:0000269|PubMed:11889103,
CC ECO:0000269|PubMed:18671734}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-
CC phosphate + NADP(+) = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-
CC 4(3H)-one 5'-phosphate + H(+) + NADPH; Xref=Rhea:RHEA:27278,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57783, ChEBI:CHEBI:58349,
CC ChEBI:CHEBI:58890, ChEBI:CHEBI:59545; EC=1.1.1.302;
CC Evidence={ECO:0000269|PubMed:11889103, ECO:0000269|PubMed:16730025,
CC ECO:0000269|PubMed:18671734};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-
CC phosphate + NAD(+) = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-
CC one 5'-phosphate + H(+) + NADH; Xref=Rhea:RHEA:27274,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57540, ChEBI:CHEBI:57945,
CC ChEBI:CHEBI:58890, ChEBI:CHEBI:59545; EC=1.1.1.302;
CC Evidence={ECO:0000269|PubMed:11889103, ECO:0000269|PubMed:16730025,
CC ECO:0000269|PubMed:18671734};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16730025}.
CC -!- MASS SPECTROMETRY: Mass=24906; Method=Electrospray;
CC Evidence={ECO:0000269|PubMed:16730025};
CC -!- MISCELLANEOUS: The protein sequence in PubMed:16730025 comes from
CC protein expressed and processed in E.coli.
CC -!- MISCELLANEOUS: Using chirally deuterated NADPH, the enzyme was shown to
CC be A-type reductase catalyzing the transfer of deuterium from the 4(R)
CC position of NADPH to the 1' (S) position of the substrate.
CC -!- SIMILARITY: Belongs to the HTP reductase family. {ECO:0000305}.
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DR EMBL; L77117; AAB98665.1; -; Genomic_DNA.
DR PIR; G64383; G64383.
DR PDB; 2AZN; X-ray; 2.70 A; A/B/C/D/E/F=6-224.
DR PDBsum; 2AZN; -.
DR AlphaFoldDB; Q58085; -.
DR SMR; Q58085; -.
DR STRING; 243232.MJ_0671; -.
DR EnsemblBacteria; AAB98665; AAB98665; MJ_0671.
DR KEGG; mja:MJ_0671; -.
DR eggNOG; arCOG01484; Archaea.
DR HOGENOM; CLU_036590_4_1_2; -.
DR InParanoid; Q58085; -.
DR OMA; CECGQEV; -.
DR PhylomeDB; Q58085; -.
DR BioCyc; MetaCyc:MON-14596; -.
DR BRENDA; 1.1.1.302; 3260.
DR UniPathway; UPA00275; -.
DR EvolutionaryTrace; Q58085; -.
DR Proteomes; UP000000805; Chromosome.
DR GO; GO:0051287; F:NAD binding; IDA:UniProtKB.
DR GO; GO:0050661; F:NADP binding; IDA:UniProtKB.
DR GO; GO:0016616; F:oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor; IDA:UniProtKB.
DR GO; GO:0046983; F:protein dimerization activity; IDA:UniProtKB.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IDA:UniProtKB.
DR Gene3D; 3.40.430.10; -; 1.
DR InterPro; IPR024072; DHFR-like_dom_sf.
DR InterPro; IPR006401; Rib_reduct_arc.
DR InterPro; IPR011549; RibD_C.
DR InterPro; IPR002734; RibDG_C.
DR Pfam; PF01872; RibD_C; 1.
DR SUPFAM; SSF53597; SSF53597; 1.
DR TIGRFAMs; TIGR01508; rib_reduct_arch; 1.
DR TIGRFAMs; TIGR00227; ribD_Cterm; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; NAD; NADP; Oxidoreductase;
KW Reference proteome; Riboflavin biosynthesis.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000305|PubMed:16730025"
FT CHAIN 2..224
FT /note="2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-
FT phosphate reductase"
FT /id="PRO_0000135944"
FT BINDING 16
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT BINDING 57
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT BINDING 61
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT BINDING 83..86
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT BINDING 134
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT BINDING 156..159
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000269|PubMed:16730025"
FT STRAND 10..18
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 35..46
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 48..54
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 55..61
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 77..81
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 92..94
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 100..104
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 110..121
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 131..133
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 136..145
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 150..155
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 157..165
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 171..178
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:2AZN"
FT HELIX 198..200
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 204..212
FT /evidence="ECO:0007829|PDB:2AZN"
FT STRAND 215..222
FT /evidence="ECO:0007829|PDB:2AZN"
SQ SEQUENCE 224 AA; 25037 MW; 4D8C15CE291E89D8 CRC64;
MVMVMEKKPY IISNVGMTLD GKLATINNDS RISCEEDLIR VHKIRANVDG IMVGIGTVLK
DDPRLTVHKI KSDRNPVRIV VDSKLRVPLN ARVLNKDAKT IIATTEDTNE EKEKKIKILE
DMGVEVVKCG RGKVDLKKLM DILYDKGIKS ILLEGGGTLN WGMFKEGLVD EVSVYIAPKI
FGGKEAPTYV DGEGFKTVDE CVKLELKNFY RLGEGIVLEF KVKK
