RIBD_BACAM
ID RIBD_BACAM Reviewed; 371 AA.
AC P70814;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 100.
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;
OS Bacillus amyloliquefaciens (Bacillus velezensis).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus amyloliquefaciens group.
OX NCBI_TaxID=1390;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=A 50;
RX PubMed=9297088;
RA Gusarov I.I., Kreneva R.A., Podcharniaev D.A., Iomantas I.U.V.,
RA Abalakina E.G., Stoinova N.V., Perumov D.A., Kozlov I.U.I.;
RT "Riboflavin biosynthetic genes in Bacillus amyloliquefaciens: primary
RT structure, organization and regulation of activity.";
RL Mol. Biol. (Mosk.) 31:446-453(1997).
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; 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.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 3/4.
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; X95955; CAA65189.1; -; Genomic_DNA.
DR PIR; T50541; T50541.
DR AlphaFoldDB; P70814; -.
DR SMR; P70814; -.
DR STRING; 692420.BAMF_2227; -.
DR eggNOG; COG0117; Bacteria.
DR eggNOG; COG1985; Bacteria.
DR UniPathway; UPA00275; UER00401.
DR UniPathway; UPA00275; UER00402.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; IEA:UniProtKB-EC.
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 3: Inferred from homology;
KW Hydrolase; Metal-binding; Multifunctional enzyme; NADP; Oxidoreductase;
KW Riboflavin biosynthesis; Zinc.
FT CHAIN 1..371
FT /note="Riboflavin biosynthesis protein RibD"
FT /id="PRO_0000171714"
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..371
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 /evidence="ECO:0000250"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 83
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 153
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 167
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 169
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 183
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 195
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 199
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
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 /evidence="ECO:0000250"
FT BINDING 290
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 292..298
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
SQ SEQUENCE 371 AA; 40166 MW; 1A90722056A6BBA9 CRC64;
MEEYYMNTAI ELARRGEGQT QPNPLVGAVV VKKRQIVGMG AHLQYGEAHA EVHAINMAGS
LAKGADLYVT LEPCSHYGKT PPCAELIMKS GIKRVFIAVE DPNPLVAGKG ITMLEEAGIE
VKTGLLRQQA EELNKMFLHF MRTGLPYVTL KAAASLDGKT ATETGDSKWI TSEAARLDAQ
QYRKSHQRIL VGAGTVKADN PSLTCRLPDA VKQPVRVILD TKLTVPETAN VLTDGAAPTW
IFTAAGSDVR KKDRLTALGI KVFTLETDRI HIPEVLSILA ENGIMSVYVE GGASVHGSFV
KAGCFDELHF YFAPILIGGT LAPSLISGEG FQSMKDVPHL QFTQITQIGP DIKLTAIPKD
GKDGDDVYRN R
