ID C6XXW3_PEDHD Unreviewed; 353 AA.
AC C6XXW3;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 07-SEP-2016, entry version 50.
DE RecName: Full=Riboflavin biosynthesis protein RibD {ECO:0000256|PIRNR:PIRNR006769};
GN OrderedLocusNames=Phep_2177 {ECO:0000313|EMBL:ACU04381.1};
OS Pedobacter heparinus (strain ATCC 13125 / DSM 2366 / CIP 104194 / JCM
OS 7457 / NBRC 12017 / NCIMB 9290 / NRRL B-14731 / HIM 762-3).
OC Bacteria; Bacteroidetes; Sphingobacteriia; Sphingobacteriales;
OC Sphingobacteriaceae; Pedobacter.
OX NCBI_TaxID=485917 {ECO:0000313|EMBL:ACU04381.1, ECO:0000313|Proteomes:UP000000852};
RN [1] {ECO:0000313|EMBL:ACU04381.1, ECO:0000313|Proteomes:UP000000852}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13125 / DSM 2366 / CIP 104194 / JCM 7457 / NBRC 12017 /
RC NCIMB 9290 / NRRL B-14731 / HIM 762-3
RC {ECO:0000313|Proteomes:UP000000852};
RX PubMed=21304637; DOI=10.4056/sigs.22138;
RA Han C., Spring S., Lapidus A., Del Rio T.G., Tice H., Copeland A.,
RA Cheng J.F., Lucas S., Chen F., Nolan M., Bruce D., Goodwin L.,
RA Pitluck S., Ivanova N., Mavromatis K., Mikhailova N., Pati A.,
RA Chen A., Palaniappan K., Land M., Hauser L., Chang Y.J.,
RA Jeffries C.C., Saunders E., Chertkov O., Brettin T., Goker M.,
RA Rohde M., Bristow J., Eisen J.A., Markowitz V., Hugenholtz P.,
RA Kyrpides N.C., Klenk H.P., Detter J.C.;
RT "Complete genome sequence of Pedobacter heparinus type strain (HIM
RT 762-3).";
RL Stand. Genomic Sci. 1:54-62(2009).
CC -!- FUNCTION: Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone
CC 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)-
CC pyrimidinedione 5'-phosphate. {ECO:0000256|PIRNR:PIRNR006769}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|PIRNR:PIRNR006769,
CC ECO:0000256|PIRSR:PIRSR006769-3};
CC Note=Binds 1 zinc ion. {ECO:0000256|PIRNR:PIRNR006769,
CC ECO:0000256|PIRSR:PIRSR006769-3};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-
CC 6-(D-ribitylamino)uracil from GTP: step 2/4.
CC {ECO:0000256|PIRNR:PIRNR006769}.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-
CC 6-(D-ribitylamino)uracil from GTP: step 3/4.
CC {ECO:0000256|PIRNR:PIRNR006769}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the HTP
CC reductase family. {ECO:0000256|PIRNR:PIRNR006769}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the cytidine and
CC deoxycytidylate deaminase family. {ECO:0000256|PIRNR:PIRNR006769}.
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DR EMBL; CP001681; ACU04381.1; -; Genomic_DNA.
DR RefSeq; WP_015807994.1; NZ_AQGK01000001.1.
DR ProteinModelPortal; C6XXW3; -.
DR STRING; 485917.Phep_2177; -.
DR EnsemblBacteria; ACU04381; ACU04381; Phep_2177.
DR KEGG; phe:Phep_2177; -.
DR PATRIC; 22881425; VBIPedHep98714_2190.
DR eggNOG; ENOG4105D1W; Bacteria.
DR eggNOG; COG0117; LUCA.
DR eggNOG; COG1985; LUCA.
DR HOGENOM; HOG000257443; -.
DR KO; K11752; -.
DR OMA; KESTIYV; -.
DR OrthoDB; POG091H01D3; -.
DR BioCyc; PHEP485917:GHL9-2200-MONOMER; -.
DR UniPathway; UPA00275; UER00401.
DR Proteomes; UP000000852; Chromosome.
DR GO; GO:0008703; F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity; IEA:InterPro.
DR GO; GO:0008835; F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity; 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_Zn-bd.
DR InterPro; IPR016193; Cytidine_deaminase-like.
DR InterPro; IPR024072; DHFR-like_dom.
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 3: Inferred from homology;
KW Complete proteome {ECO:0000313|Proteomes:UP000000852};
KW Hydrolase {ECO:0000256|PIRNR:PIRNR006769};
KW Metal-binding {ECO:0000256|PIRNR:PIRNR006769,
KW ECO:0000256|PIRSR:PIRSR006769-3};
KW NADP {ECO:0000256|PIRNR:PIRNR006769, ECO:0000256|PIRSR:PIRSR006769-2};
KW Oxidoreductase {ECO:0000256|PIRNR:PIRNR006769};
KW Reference proteome {ECO:0000313|Proteomes:UP000000852};
KW Riboflavin biosynthesis {ECO:0000256|PIRNR:PIRNR006769};
KW Zinc {ECO:0000256|PIRNR:PIRNR006769, ECO:0000256|PIRSR:PIRSR006769-3}.
FT DOMAIN 1 131 CMP/dCMP-type deaminase.
FT {ECO:0000259|PROSITE:PS51747}.
FT ACT_SITE 52 52 Proton donor. {ECO:0000256|PIRSR:
FT PIRSR006769-1}.
FT METAL 50 50 Zinc; catalytic. {ECO:0000256|PIRSR:
FT PIRSR006769-3}.
FT METAL 83 83 Zinc; catalytic. {ECO:0000256|PIRSR:
FT PIRSR006769-3}.
FT METAL 92 92 Zinc; catalytic. {ECO:0000256|PIRSR:
FT PIRSR006769-3}.
FT BINDING 162 162 NADP; via amide nitrogen and carbonyl
FT oxygen. {ECO:0000256|PIRSR:PIRSR006769-
FT 2}.
FT BINDING 178 178 NADP. {ECO:0000256|PIRSR:PIRSR006769-2}.
FT BINDING 192 192 Substrate. {ECO:0000256|PIRSR:
FT PIRSR006769-2}.
FT BINDING 204 204 NADP. {ECO:0000256|PIRSR:PIRSR006769-2}.
FT BINDING 208 208 NADP. {ECO:0000256|PIRSR:PIRSR006769-2}.
FT BINDING 212 212 Substrate; via amide nitrogen.
FT {ECO:0000256|PIRSR:PIRSR006769-2}.
FT BINDING 215 215 Substrate. {ECO:0000256|PIRSR:
FT PIRSR006769-2}.
FT BINDING 291 291 Substrate. {ECO:0000256|PIRSR:
FT PIRSR006769-2}.
SQ SEQUENCE 353 AA; 39465 MW; 131FBE71AB265435 CRC64;
MTNELYMQRC LELAAMGMGN VSPNPMVGCV IVSDGKIIGE GYHARFGEAH AEVNAINSVV
HNYGNTAETL LAAATAYVSL EPCAHFGKTP PCADLLIKHR IKKVVIGNTD PFDGVNGKGI
EKLKNAGIEV VSGVLEAECS QLNRRFFTRI GQQHPYIILK WATSANGYFA PENTTQQWIS
GPEAKKLVHK WRTEEDAVLV GRLTAMADNP RLTVREWYGR NPVRIVVDRH LQVPSSHHIY
NKEAKTIIFN EQKTDVQENI HFIQMEDMQH YLPQKIAFQL YLMDIASVII EGGAQVLNQF
IQARLWDEAR VFRSAVSWPA GIPSPELNLQ SCAITDQFPI GKDQLTIYKN NPS
//
