RIBD_ECOLI
ID RIBD_ECOLI Reviewed; 367 AA.
AC P25539; Q2MC12;
DT 01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1992, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Riboflavin biosynthesis protein RibD;
DE Includes:
DE RecName: Full=Diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE EC=3.5.4.26 {ECO:0000269|PubMed:9068650};
DE AltName: Full=Riboflavin-specific deaminase;
DE Includes:
DE RecName: Full=5-amino-6-(5-phosphoribosylamino)uracil reductase;
DE EC=1.1.1.193 {ECO:0000269|PubMed:9068650};
DE AltName: Full=HTP reductase;
GN Name=ribD; Synonyms=ribG, ybaE; OrderedLocusNames=b0414, JW0404;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1406588; DOI=10.1007/bf00538702;
RA Taura T., Ueguchi C., Shiba K., Ito K.;
RT "Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive
RT growth of Escherichia coli and suppression of the secY24 mutation.";
RL Mol. Gen. Genet. 234:429-432(1992).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RX PubMed=9068650; DOI=10.1128/jb.179.6.2022-2028.1997;
RA Richter G., Fischer M., Krieger C., Eberhardt S., Luttgen H.,
RA Gerstenschlager I., Bacher A.;
RT "Biosynthesis of riboflavin: characterization of the bifunctional
RT deaminase-reductase of Escherichia coli and Bacillus subtilis.";
RL J. Bacteriol. 179:2022-2028(1997).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH RIBOSE-5-PHOSPHATE
RP AND NADP, AND SUBUNIT.
RX PubMed=17765262; DOI=10.1016/j.jmb.2006.12.009;
RA Stenmark P., Moche M., Gurmu D., Nordlund P.;
RT "The crystal structure of the bifunctional deaminase/reductase RibD of the
RT riboflavin biosynthetic pathway in Escherichia coli: implications for the
RT reductive mechanism.";
RL J. Mol. Biol. 373:48-64(2007).
CC -!- FUNCTION: Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-
CC phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-pyrimidinedione 5'-
CC phosphate. {ECO:0000269|PubMed:9068650}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine +
CC H(+) + H2O = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NH4(+);
CC Xref=Rhea:RHEA:21868, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:28938, ChEBI:CHEBI:58453, ChEBI:CHEBI:58614; EC=3.5.4.26;
CC Evidence={ECO:0000269|PubMed:9068650};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:21869;
CC Evidence={ECO:0000269|PubMed:9068650};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-
CC amino-6-(5-phospho-D-ribosylamino)uracil + H(+) + NADPH;
CC Xref=Rhea:RHEA:17845, ChEBI:CHEBI:15378, ChEBI:CHEBI:57783,
CC ChEBI:CHEBI:58349, ChEBI:CHEBI:58421, ChEBI:CHEBI:58453;
CC EC=1.1.1.193; Evidence={ECO:0000269|PubMed:9068650};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:17846;
CC Evidence={ECO:0000269|PubMed:9068650};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105; Evidence={ECO:0000250};
CC Note=Binds 1 zinc ion. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 2/4. {ECO:0000305|PubMed:9068650}.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 3/4. {ECO:0000305|PubMed:9068650}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:17765262}.
CC -!- INTERACTION:
CC P25539; P24182: accC; NbExp=3; IntAct=EBI-552457, EBI-542308;
CC -!- SIMILARITY: In the N-terminal section; belongs to the cytidine and
CC deoxycytidylate deaminase family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the HTP reductase
CC family. {ECO:0000305}.
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DR EMBL; X64395; CAA45735.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40170.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73517.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76194.1; -; Genomic_DNA.
DR PIR; S26201; S26201.
DR RefSeq; NP_414948.1; NC_000913.3.
DR RefSeq; WP_001150457.1; NZ_SSZK01000009.1.
DR PDB; 2G6V; X-ray; 2.60 A; A/B=2-367.
DR PDB; 2O7P; X-ray; 3.00 A; A/B=2-367.
DR PDB; 2OBC; X-ray; 3.00 A; A/B=2-367.
DR PDBsum; 2G6V; -.
DR PDBsum; 2O7P; -.
DR PDBsum; 2OBC; -.
DR AlphaFoldDB; P25539; -.
DR SMR; P25539; -.
DR BioGRID; 4263249; 26.
DR BioGRID; 849992; 6.
DR DIP; DIP-10708N; -.
DR IntAct; P25539; 34.
DR STRING; 511145.b0414; -.
DR jPOST; P25539; -.
DR PaxDb; P25539; -.
DR PRIDE; P25539; -.
DR EnsemblBacteria; AAC73517; AAC73517; b0414.
DR EnsemblBacteria; BAE76194; BAE76194; BAE76194.
DR GeneID; 945620; -.
DR KEGG; ecj:JW0404; -.
DR KEGG; eco:b0414; -.
DR PATRIC; fig|1411691.4.peg.1863; -.
DR EchoBASE; EB1297; -.
DR eggNOG; COG0117; Bacteria.
DR eggNOG; COG1985; Bacteria.
DR HOGENOM; CLU_036590_1_2_6; -.
DR InParanoid; P25539; -.
DR OMA; DEMYMAR; -.
DR PhylomeDB; P25539; -.
DR BioCyc; EcoCyc:RIBOFLAVINSYNDEAM-MON; -.
DR BioCyc; MetaCyc:RIBOFLAVINSYNDEAM-MON; -.
DR BRENDA; 1.1.1.193; 2026.
DR BRENDA; 3.5.4.26; 2026.
DR SABIO-RK; P25539; -.
DR UniPathway; UPA00275; UER00401.
DR UniPathway; UPA00275; UER00402.
DR EvolutionaryTrace; P25539; -.
DR PRO; PR:P25539; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IDA:EcoCyc.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IDA:EcoCyc.
DR GO; GO:0050661; F:NADP binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IDA:EcoCyc.
DR Gene3D; 3.40.430.10; -; 1.
DR InterPro; IPR016192; APOBEC/CMP_deaminase_Zn-bd.
DR InterPro; IPR002125; CMP_dCMP_dom.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR024072; DHFR-like_dom_sf.
DR InterPro; IPR004794; Eubact_RibD.
DR InterPro; IPR011549; RibD_C.
DR InterPro; IPR002734; RibDG_C.
DR Pfam; PF00383; dCMP_cyt_deam_1; 1.
DR Pfam; PF01872; RibD_C; 1.
DR PIRSF; PIRSF006769; RibD; 1.
DR SUPFAM; SSF53597; SSF53597; 1.
DR SUPFAM; SSF53927; SSF53927; 1.
DR TIGRFAMs; TIGR00326; eubact_ribD; 1.
DR TIGRFAMs; TIGR00227; ribD_Cterm; 1.
DR PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Multifunctional enzyme; NADP;
KW Oxidoreductase; Reference proteome; Riboflavin biosynthesis; Zinc.
FT CHAIN 1..367
FT /note="Riboflavin biosynthesis protein RibD"
FT /id="PRO_0000171721"
FT DOMAIN 1..123
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT REGION 1..145
FT /note="Deaminase"
FT REGION 146..367
FT /note="Reductase"
FT ACT_SITE 52
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 84
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 161..164
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 168
FT /ligand="substrate"
FT BINDING 170
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 184
FT /ligand="substrate"
FT BINDING 196
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 200
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 204
FT /ligand="substrate"
FT BINDING 207
FT /ligand="substrate"
FT BINDING 234
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 299
FT /ligand="substrate"
FT BINDING 301..304
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT HELIX 2..14
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 15..17
FT /evidence="ECO:0007829|PDB:2OBC"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 28..33
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 51..59
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 85..91
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 96..100
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 111..117
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 122..124
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 128..134
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 136..143
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 148..156
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 174..185
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 187..193
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 194..200
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 208..210
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 214..217
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 228..232
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 247..249
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 251..257
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 267..271
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 281..290
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 295..298
FT /evidence="ECO:0007829|PDB:2OBC"
FT HELIX 302..311
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 315..323
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:2OBC"
FT STRAND 359..365
FT /evidence="ECO:0007829|PDB:2OBC"
SQ SEQUENCE 367 AA; 40338 MW; B19CEF474D48D14D CRC64;
MQDEYYMARA LKLAQRGRFT THPNPNVGCV IVKDGEIVGE GYHQRAGEPH AEVHALRMAG
EKAKGATAYV TLEPCSHHGR TPPCCDALIA AGVARVVASM QDPNPQVAGR GLYRLQQAGI
DVSHGLMMSE AEQLNKGFLK RMRTGFPYIQ LKLGASLDGR TAMASGESQW ITSPQARRDV
QLLRAQSHAI LTSSATVLAD DPALTVRWSE LDEQTQALYP QQNLRQPIRI VIDSQNRVTP
VHRIVQQPGE TWFARTQEDS REWPETVRTL LIPEHKGHLD LVVLMMQLGK QQINSIWVEA
GPTLAGALLQ AGLVDELIVY IAPKLLGSDA RGLCTLPGLE KLADAPQFKF KEIRHVGPDV
CLHLVGA
