RIBD_MYCTU
ID RIBD_MYCTU Reviewed; 339 AA.
AC P9WPH1; L0T9J7; P71677;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 46.
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=Rv1409; ORFNames=MTCY21B4.26;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
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:0000250}.
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 -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
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; AL123456; CCP44168.1; -; Genomic_DNA.
DR PIR; F70901; F70901.
DR RefSeq; NP_215925.1; NC_000962.3.
DR RefSeq; WP_003898867.1; NZ_NVQJ01000038.1.
DR AlphaFoldDB; P9WPH1; -.
DR SMR; P9WPH1; -.
DR STRING; 83332.Rv1409; -.
DR PaxDb; P9WPH1; -.
DR DNASU; 886721; -.
DR GeneID; 886721; -.
DR KEGG; mtu:Rv1409; -.
DR TubercuList; Rv1409; -.
DR eggNOG; COG0117; Bacteria.
DR eggNOG; COG1985; Bacteria.
DR OMA; PYIILKW; -.
DR PhylomeDB; P9WPH1; -.
DR UniPathway; UPA00275; UER00401.
DR UniPathway; UPA00275; UER00402.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
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: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; 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 PROSITE; PS00903; CYT_DCMP_DEAMINASES_1; 1.
DR PROSITE; PS51747; CYT_DCMP_DEAMINASES_2; 1.
PE 1: Evidence at protein level;
KW Hydrolase; Metal-binding; Multifunctional enzyme; NADP; Oxidoreductase;
KW Reference proteome; Riboflavin biosynthesis; Zinc.
FT CHAIN 1..339
FT /note="Riboflavin biosynthesis protein RibD"
FT /id="PRO_0000171723"
FT DOMAIN 7..129
FT /note="CMP/dCMP-type deaminase"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT REGION 1..152
FT /note="Deaminase"
FT REGION 153..339
FT /note="Reductase"
FT ACT_SITE 59
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 82
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 168..171
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 175
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 177
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 191
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 203
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 207
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
FT BINDING 211
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 214
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 272
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 274..280
FT /ligand="NADP(+)"
FT /ligand_id="ChEBI:CHEBI:58349"
FT /evidence="ECO:0000250"
SQ SEQUENCE 339 AA; 35367 MW; 1DC0A1B8E7EC08B4 CRC64;
MNVEQVKSID EAMGLAIEHS YQVKGTTYPK PPVGAVIVDP NGRIVGAGGT EPAGGDHAEV
VALRRAGGLA AGAIVVVTME PCNHYGKTPP CVNALIEARV GTVVYAVADP NGIAGGGAGR
LSAAGLQVRS GVLAEQVAAG PLREWLHKQR TGLPHVTWKY ATSIDGRSAA ADGSSQWISS
EAARLDLHRR RAIADAILVG TGTVLADDPA LTARLADGSL APQQPLRVVV GKRDIPPEAR
VLNDEARTMM IRTHEPMEVL RALSDRTDVL LEGGPTLAGA FLRAGAINRI LAYVAPILLG
GPVTAVDDVG VSNITNALRW QFDSVEKVGP DLLLSLVAR
