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RIBD_BUCBP
ID   RIBD_BUCBP              Reviewed;         372 AA.
AC   Q89AB0;
DT   13-APR-2004, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2003, sequence version 1.
DT   03-AUG-2022, entry version 113.
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; OrderedLocusNames=bbp_408;
OS   Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Erwiniaceae; Buchnera.
OX   NCBI_TaxID=224915;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Bp;
RX   PubMed=12522265; DOI=10.1073/pnas.0235981100;
RA   van Ham R.C.H.J., Kamerbeek J., Palacios C., Rausell C., Abascal F.,
RA   Bastolla U., Fernandez J.M., Jimenez L., Postigo M., Silva F.J.,
RA   Tamames J., Viguera E., Latorre A., Valencia A., Moran F., Moya A.;
RT   "Reductive genome evolution in Buchnera aphidicola.";
RL   Proc. Natl. Acad. Sci. U.S.A. 100:581-586(2003).
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   -!- 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; AE016826; AAO27119.1; -; Genomic_DNA.
DR   RefSeq; WP_011091520.1; NC_004545.1.
DR   AlphaFoldDB; Q89AB0; -.
DR   SMR; Q89AB0; -.
DR   STRING; 224915.bbp_408; -.
DR   EnsemblBacteria; AAO27119; AAO27119; bbp_408.
DR   GeneID; 56470945; -.
DR   KEGG; bab:bbp_408; -.
DR   eggNOG; COG0117; Bacteria.
DR   eggNOG; COG1985; Bacteria.
DR   HOGENOM; CLU_036590_1_2_6; -.
DR   OMA; DEMYMAR; -.
DR   OrthoDB; 1775351at2; -.
DR   UniPathway; UPA00275; UER00401.
DR   UniPathway; UPA00275; UER00402.
DR   Proteomes; UP000000601; 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; 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   Reference proteome; Riboflavin biosynthesis; Zinc.
FT   CHAIN           1..372
FT                   /note="Riboflavin biosynthesis protein RibD"
FT                   /id="PRO_0000171716"
FT   DOMAIN          1..122
FT                   /note="CMP/dCMP-type deaminase"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01083"
FT   REGION          1..145
FT                   /note="Deaminase"
FT   REGION          146..372
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         154
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
FT   BINDING         168
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         170
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
FT   BINDING         184
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         196
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
FT   BINDING         200
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
FT   BINDING         204
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         207
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         236
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
FT   BINDING         301
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         303..309
FT                   /ligand="NADP(+)"
FT                   /ligand_id="ChEBI:CHEBI:58349"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   372 AA;  41598 MW;  6BB07CE7E9016C7A CRC64;
     MKDIFYMKKA IKLAKKGSLT TSPNPNVGCI IVNNNIIVGS GWHKKTGMKH AEIYALKTSG
     EKAKGATAYI TLEPCSHFGK TPPCCVALTK YGISRVVIAT LDPNPKVSGN GVKWLKKHGI
     LVTIGTLSKE SIKINKGFFQ RMTTGIPWIK LKLASSIDGR TALNNGKSKW ITSDKARHDV
     QHVREKSDAI ISSSETILFD NPLLTVRNTN NNDNNQKLLK HSKTFLKQPI RVIIDSKNRI
     TPSHKCIKQP GLLFLIRIHS DNNIWPSHIK QIILNNKSKK IDLIDLVKML AKYQINNILI
     EAGPSLSSSF LKLNIINELI IYIAPKILGN YAKPLFFLEN YSNLSDVPQF KFEKITQIGK
     DLKLILTKHN SS
 
 
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