RIBD_BACSU
ID RIBD_BACSU Reviewed; 361 AA.
AC P17618;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1990, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Riboflavin biosynthesis protein RibD;
DE Includes:
DE RecName: Full=Diaminohydroxyphosphoribosylaminopyrimidine deaminase;
DE Short=DRAP deaminase;
DE EC=3.5.4.26;
DE AltName: Full=Riboflavin-specific deaminase;
DE Includes:
DE RecName: Full=5-amino-6-(5-phosphoribosylamino)uracil reductase;
DE EC=1.1.1.193;
DE AltName: Full=HTP reductase;
GN Name=ribD; Synonyms=ribG; OrderedLocusNames=BSU23280;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / SHGW;
RA Mironov V.N.;
RL Thesis (1989), USSR Academy of Sciences, Russia.
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168 / Marburg / ATCC 6051 / DSM 10 / JCM 1465 / NBRC 13719 / NCIMB
RC 3610 / NRRL NRS-744 / VKM B-501;
RX PubMed=7934829; DOI=10.1111/j.1365-2958.1993.tb02670.x;
RA Sorokin A.V., Zumstein E., Azevedo V., Ehrlich S.D., Serror P.;
RT "The organization of the Bacillus subtilis 168 chromosome region between
RT the spoVA and serA genetic loci, based on sequence data.";
RL Mol. Microbiol. 10:385-395(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-12.
RC STRAIN=168 / SHGW;
RX PubMed=2112225;
RA Mironov V.N., Perumov D.A., Kraev A.S., Stepanov A.I., Skriabin K.G.;
RT "Unusual structure of the regulatory region of the riboflavin biosynthesis
RT operon in Bacillus subtilis.";
RL Mol. Biol. (Mosk.) 24:256-261(1990).
RN [5]
RP CHARACTERIZATION.
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 (2.41 ANGSTROMS) IN COMPLEXES WITH ZINC AND NADP,
RP COFACTOR, AND SUBUNIT.
RX PubMed=16308316; DOI=10.1074/jbc.m510254200;
RA Chen S.-C., Chang Y.-C., Lin C.-H., Lin C.-H., Liaw S.-H.;
RT "Crystal structure of a bifunctional deaminase and reductase from Bacillus
RT subtilis involved in riboflavin biosynthesis.";
RL J. Biol. Chem. 281:7605-7613(2006).
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.
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 -!- 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;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:16308316};
CC Note=Binds 1 zinc ion. {ECO:0000269|PubMed:16308316};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 2/4.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 3/4.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16308316}.
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; X51510; CAA35878.1; -; Genomic_DNA.
DR EMBL; L09228; AAA67481.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB14260.1; -; Genomic_DNA.
DR PIR; S45543; PN0100.
DR RefSeq; NP_390209.1; NC_000964.3.
DR RefSeq; WP_004398763.1; NZ_JNCM01000036.1.
DR PDB; 2B3Z; X-ray; 2.41 A; A/B/C/D=1-361.
DR PDB; 2D5N; X-ray; 2.97 A; A/B/C/D=1-361.
DR PDB; 3EX8; X-ray; 2.56 A; A/B/C/D=1-361.
DR PDB; 4G3M; X-ray; 2.56 A; A/B/C/D=1-361.
DR PDBsum; 2B3Z; -.
DR PDBsum; 2D5N; -.
DR PDBsum; 3EX8; -.
DR PDBsum; 4G3M; -.
DR AlphaFoldDB; P17618; -.
DR SMR; P17618; -.
DR BioGRID; 856545; 1.
DR STRING; 224308.BSU23280; -.
DR PaxDb; P17618; -.
DR PRIDE; P17618; -.
DR EnsemblBacteria; CAB14260; CAB14260; BSU_23280.
DR GeneID; 938945; -.
DR KEGG; bsu:BSU23280; -.
DR PATRIC; fig|224308.179.peg.2535; -.
DR eggNOG; COG0117; Bacteria.
DR eggNOG; COG1985; Bacteria.
DR InParanoid; P17618; -.
DR OMA; PYIILKW; -.
DR PhylomeDB; P17618; -.
DR BioCyc; BSUB:BSU23280-MON; -.
DR BRENDA; 1.1.1.193; 658.
DR BRENDA; 3.5.4.26; 658.
DR UniPathway; UPA00275; UER00401.
DR UniPathway; UPA00275; UER00402.
DR EvolutionaryTrace; P17618; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IBA:GO_Central.
DR GO; GO:0050661; F:NADP binding; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniPathway.
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..361
FT /note="Riboflavin biosynthesis protein RibD"
FT /id="PRO_0000171715"
FT DOMAIN 1..122
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT REGION 1..144
FT /note="Deaminase"
FT REGION 145..361
FT /note="Reductase"
FT ACT_SITE 51
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 49
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 83
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 153
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 169
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 183
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 195
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 199
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 203
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 206
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 221
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT BINDING 290
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 292..298
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT HELIX 2..13
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 14..16
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 19..23
FT /evidence="ECO:0007829|PDB:2D5N"
FT STRAND 27..41
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 50..58
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 66..71
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 78..80
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 83..90
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:2B3Z"
FT TURN 104..108
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 109..115
FT /evidence="ECO:0007829|PDB:2B3Z"
FT TURN 116..118
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 127..133
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 135..143
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 147..155
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 158..161
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 173..179
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 182..185
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 186..192
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 193..199
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:3EX8"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 230..233
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 249..256
FT /evidence="ECO:0007829|PDB:2B3Z"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 261..264
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 266..269
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 272..281
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 286..291
FT /evidence="ECO:0007829|PDB:2B3Z"
FT HELIX 293..302
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 306..315
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 320..322
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:2B3Z"
FT TURN 334..336
FT /evidence="ECO:0007829|PDB:3EX8"
FT STRAND 339..348
FT /evidence="ECO:0007829|PDB:2B3Z"
FT STRAND 351..358
FT /evidence="ECO:0007829|PDB:2B3Z"
SQ SEQUENCE 361 AA; 39305 MW; DA836930BFDECA3B CRC64;
MEEYYMKLAL DLAKQGEGQT ESNPLVGAVV VKDGQIVGMG AHLKYGEAHA EVHAIHMAGA
HAEGADIYVT LEPCSHYGKT PPCAELIINS GIKRVFVAMR DPNPLVAGRG ISMMKEAGIE
VREGILADQA ERLNEKFLHF MRTGLPYVTL KAAASLDGKI ATSTGDSKWI TSEAARQDAQ
QYRKTHQSIL VGVGTVKADN PSLTCRLPNV TKQPVRVILD TVLSIPEDAK VICDQIAPTW
IFTTARADEE KKKRLSAFGV NIFTLETERI QIPDVLKILA EEGIMSVYVE GGSAVHGSFV
KEGCFQEIIF YFAPKLIGGT HAPSLISGEG FQSMKDVPLL QFTDITQIGR DIKLTAKPTK
E
