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Rule : Riboflavin biosynthesis protein RibD (RIBD)

Rule Description

ID NRULE_0202
Rule name RIBD
Created 2013-04-09
Protein name
Protein name
Full
Riboflavin biosynthesis protein RibD
Gene name ribD
Rule Trigger TIGRFAMs; TIGR00326; hit=1ANDTIGRFAMs; TIGR00227; hit=1
Cross Reference
Gene Ontology
GO
GO:0008703, F:5-amino-6-(5-phosphoribosylamino)uracil reductase activity, IDA:EcoCyc
GO:0008835, F:diaminohydroxyphosphoribosylaminopyrimidine deaminase activity, IDA:EcoCyc
GO:0050661, F:NADP binding, IDA:EcoCyc
GO:0008270, F:zinc ion binding, IEA:InterPro
GO:0009231, P:riboflavin biosynthetic process, IDA:EcoCyc
Phylogenomic databases
eggNOG
COG0117, -
HOGENOM
HOG000257442, -
KO
K11752, -
ProtClustDB
PRK10786, -
Enzyme and pathway databases
BioCyc
MetaCyc:RIBOFLAVINSYNDEAM-MONOMER, -
UniPathway
UPA00275, UER00401
UPA00275, UER00402
Family and domain databases
InterPro
IPR016192, APOBEC/CMP_deaminase_Zn-bd
IPR002125, CMP_dCMP_Zn-bd
IPR016193, Cytidine_deaminase-like
IPR024072, DHFR-like_dom
IPR004794, Eubact_RibD
IPR011549, RibD_C
IPR002734, RibDG_C
Pfam
PF00383, dCMP_cyt_deam_1, 1
PF01872, RibD_C, 1
PIRSF
PIRSF006769, RibD, 1
TIGRFAMs
TIGR00326, eubact_ribD, 1
TIGR00227, ribD_Cterm, 1
PROSITE
PS00903, CYT_DCMP_DEAMINASES, 1
Feature
P25539 Escherichia coli (strain K12).
NP_BIND161 - 164NADP.
NP_BIND301 - 304NADP.
ACT_SITE52Proton donor (By similarity).
METAL50Zinc; catalytic (By similarity).
METAL75Zinc; catalytic (By similarity).
METAL84Zinc; catalytic (By similarity).
BINDING168Substrate.
BINDING170NADP.
BINDING184Substrate.
BINDING196NADP.
BINDING200NADP.
BINDING204Substrate; via amide nitrogen.
BINDING207Substrate.
BINDING234NADP.
BINDING299Substrate.
General annotation
Function
Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
Catalytic activity
2,5-diamino-6-hydroxy-4-(5- phosphoribosylamino)pyrimidine + H(2)O = 5-amino-6-(5- phosphoribosylamino)uracil + NH(3)
5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP(+) = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
Cofactor
Binds 1 zinc ion (By similarity)
Pathway
Cofactor biosynthesis; riboflavin biosynthesis; 5-amino- 6-(D-ribitylamino)uracil from GTP: step 2/4
Cofactor biosynthesis; riboflavin biosynthesis; 5-amino- 6-(D-ribitylamino)uracil from GTP: step 3/4
Subunit structure
Homodimer
Sequence similarities
In the N-terminal section; belongs to the cytidine and deoxycytidylate deaminase family
In the C-terminal section; belongs to the HTP reductase family
Reference
P25539 Escherichia coli (strain K12).
1406588
Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation. (Mol Gen Genet. 1992)
9278503
The complete genome sequence of Escherichia coli K-12. (Science. 1997)
16738553
Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. (Mol Syst Biol. 2006)
9068650
Biosynthesis of riboflavin: characterization of the bifunctional deaminase-reductase of Escherichia coli and Bacillus subtilis. (J Bacteriol. 1997)
17765262
The crystal structure of the bifunctional deaminase/reductase RibD of the riboflavin biosynthetic pathway in Escherichia coli: implications for the reductive mechanism. (J Mol Biol. 2007)



Related Function

Function name
Riboflavin biosynthesis

CDS

Data Download
Scientific name NBRC No. CDS Product name
Acaryochloris marina102967AM1_3853riboflavin biosynthesis protein RibD
Acholeplasma laidlawii14400ACL_1106riboflavin biosynthesis protein
Acidiphilium multivorum100883ACMV_23660diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Acidithiobacillus ferrooxidansLferr_0473riboflavin biosynthesis protein RibD
Acinetobacter radioresistens102413ACRAD_28_00280diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Acinetobacter sp.100985ACT4_010_00390riboflavin biosynthesis protein RibD
Actinoplanes missouriensis102363AMIS_61960putative riboflavin/cytosine deaminase
Aerococcus viridans12219HMPREF0061_1455riboflavin biosynthesis protein RibD
Alicyclobacillus acidocaldarius subsp. acidocaldarius15652Aaci_0936riboflavin biosynthesis protein RibD
Alteromonas macleodii102226MASE_12425Riboflavin biosynthesis protein RibD
Anoxybacillus flavithermus15317Aflv_1015Riboflavin-specific pyrimidine reductase/deaminase
Aquifex aeolicusaq_138riboflavin specific deaminase
Ardenticatena maritimaARMA_1602diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase
Azorhizobium caulinodans14845AZC_1263riboflavin biosynthesis protein
Bacillus amyloliquefaciens15535BAMF_2227fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Bacillus atrophaeus13721BATRMS_17_02780fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Bacillus cereus15305BC_3387Diaminohydroxyphosphoribosylaminopyrimidine deaminase
BC_4109Diaminohydroxyphosphoribosylaminopyrimidine deaminase
Bacillus licheniformis12200BL01891riboflavin-specific deaminase
Bacillus licheniformis12195BLi02475bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
Bacillus mojavensis15718GYU_39_00230riboflavin biosynthesis protein RibD
Bacillus mycoides101228bmyco0001_37360RibD (Riboflavin-specific deaminase)
Bacillus pseudomycoides101232bpmyx0001_35910RibD (Riboflavin-specific deaminase)
Bacillus psychrosaccharolyticus101233WYK_005_00080riboflavin biosynthesis protein RibD
Bacillus pumilus12092BAT_0978riboflavin biosynthesis protein RibD
BAT_3394riboflavin biosynthesis protein RibD
Bacillus subtilis3134BSU6633_14187fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Bacillus subtilis subsp. subtilis13719BSU23280fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Bacillus thuringiensis101235bthur0008_30970Riboflavin biosynthesis protein
bthur0008_39020RibD (Riboflavin-specific deaminase)
Bacillus vallismortis101236BvalD_010100002612fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Balneola vulgarisB155_RS0110995riboflavin biosynthesis protein RibD
Bradyrhizobium diazoefficiens14792bll5031riboflavin biosynthesis protein
Brevibacillus brevis100599BBR47_48140riboflavin biosynthesis protein RibD
Calditerrivibrio nitroreducens101217Calni_1660riboflavin biosynthesis protein RibD
Candidatus Solibacter usitatusAcid_42225-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase
Chlamydia trachomatisCTL0099Riboflavin biosynthesis protein (diaminohydroxyphosphoribosylaminopyrimidine deaminase)
Chloracidobacterium thermophilum BCabther_A0264riboflavin biosynthesis protein RibD
Chlorobaculum tepidum103806CT0747riboflavin biosynthesis protein RibD
Chlorobium limicola103803Clim_0829riboflavin biosynthesis protein RibD
Chromobacterium violaceum12614CV_1290diaminohydroxyphosphoribosylaminopyrimidine deaminase
Chrysiogenes arsenatisP304_RS15490hypothetical protein
Chthonomonas calidiroseaCCALI_00796riboflavin biosynthesis protein RibD
Clostridium acetobutylicum13948CA_C0590Riboflavin biosynthesis protein RIBD (pirimidine deaminase and pirimidine reductase)
Clostridium clariflavum101661Clocl_1124diaminohydroxyphosphoribosylaminopyrimidine deaminase, 5-amino-6-(5-phosphoribosylamino)uracil reductase
Clostridium kluyveri12016CKR_1904hypothetical protein
Clostridium thermocellum103400Cthe_0104riboflavin biosynthesis protein RibD
Conexibacter woesei100937Cwoe_3708riboflavin biosynthesis protein RibD
Congregibacter litoralis104960KT71_01410riboflavin biosynthesis protein RibD
Cupriavidus metallidurans102507Rmet_2688fused diaminohydroxyphosphoribosylaminopyrimidine deaminase ; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Cystobacter fuscus100088D187_004612Diaminohydroxyphosphoribosylaminopyrimidine deaminase
Deferribacter desulfuricans101012DEFDS_1096bifunctional riboflavin biosynthesis protein RibD
Dehalococcoides mccartyiDehaBAV1_10015-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase
Edwardsiella tarda105688ET1_20_00760diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Endomicrobium proavitumEpro_0586Diaminohydroxyphosphoribosylaminopyrimidine deaminase
Enterobacter aerogenes13534EAE_12540bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Enterobacter cloacae subsp. cloacae13535ECL_01172bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Enterobacter hormaechei105718HMPREF9086_1490riboflavin biosynthesis protein RibD
Escherichia coli3972EcolC_3219riboflavin biosynthesis protein RibD
Escherichia coli13500WFL_02390bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Escherichia coli12713Y75_0403fused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5-amino-6-(5-phosphoribosylamino) uracil reductase
Escherichia fergusonii102419EFER_2611fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Escherichia hermannii105704EH105704_10_00130diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Fischerella sp.PCC9339_RS01271505-amino-6-(5-phosphoribosylamino)uracil reductase
Frateuria aurantia3245Fraau_0448riboflavin biosynthesis protein RibD
Fusobacterium nucleatum subsp. NucleatumFN1506Diaminohydroxyphosphoribosylaminopyrimidine deaminase
Gemmata obscuriglobusGEMOB_RS35630riboflavin biosynthesis protein RibD
Gloeobacter violaceusgll1250riboflavin biosynthesis protein
Halobacillus halophilus102448HBHAL_4681riboflavin biosynthesis protein RibD
Halomonas elongata15536HELO_3591riboflavin biosynthesis protein RibD
Haloplasma contractileHLPCO_001291Riboflavin biosynthesis protein RibD
Herpetosiphon aurantiacusHaur_2423riboflavin biosynthesis protein RibD
Hylemonella gracilis14920HGR_09483riboflavin biosynthesis protein RibD
Ignavibacterium album101810IALB_2406Pyrimidine deaminase
Klebsiella pneumoniae14438KPR_4355
Klebsiella pneumoniae subsp. rhinoscleromatis105682HMPREF0484_2615riboflavin biosynthesis protein RibD
Ktedonobacter racemiferKrac_1420riboflavin biosynthesis protein RibD
Krac_1702riboflavin biosynthesis protein RibD
Krac_2906riboflavin biosynthesis protein RibD
Kyrpidia tusciae15312Btus_1826riboflavin biosynthesis protein RibD
Labrenzia aggregata16684SIAM614_10428riboflavin biosynthesis protein
Limnochorda pilosa110152LIP_32995-amino-6-(5-phosphoribosylamino)uracil reductase
Magnetospirillum gryphiswaldense15271MGR_2798Riboflavin biosynthesis protein
Magnetospirillum magnetotacticum15272Magn03009108COG1985: Pyrimidine reductase, riboflavin biosynthesis
Marinomonas mediterranea103028Marme_0498riboflavin biosynthesis protein RibD
Meiothermus ruber106122Mrub_1255riboflavin biosynthesis protein RibD
Meiothermus silvanus106475Mesil_3462hypothetical protein
Micromonospora aurantiaca16155Micau_2356riboflavin biosynthesis protein RibD
Nakamurella multipartita105858Namu_0753riboflavin biosynthesis protein RibD
Nitrosomonas europaea14298NE0793Riboflavin biosynthesis bifunctional RibD
Nitrospina gracilisNITGR_910041fused diaminohydroxyphosphoribosylaminopyrimidine deaminase;5-amino-6-(5-phosphoribosylamino) uracil reductase
Nostoc sp.all0082 ribD gene product
Oscillibacter valericigenes101213OBV_01230diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Paenibacillus alvei3343PAV_1c08510riboflavin biosynthesis protein RibD
PAV_3c05330riboflavin biosynthesis protein RibD
Paenibacillus peoriae15541PpeoK3_010100008886riboflavin biosynthesis protein (diaminohydroxyphosphoribosylaminopyrimidine deaminase (riboflavin-specific deaminase) and 5-amino-6-(5-phosphoribosylamino)uracil reductase)
Paenibacillus polymyxa15309PPT_236455-amino-6-(5-phosphoribosylamino)uracil reductase
Pelobacter carbinolicus103641Pcar_14452, 5-diamino-6-(5'-phosphoribosylamino)-4-(3H)-pyrimidinone deaminase and 5-amino-6-(5'-phosphoribosylamino)uracil reductase
Pelobacter propionicus103807Ppro_15965-amino-6-(5-phosphoribosylamino)uracil reductase
Phaeobacter gallaeciensis16654PGA1_c08870riboflavin biosynthesis protein RibD
Photobacterium damselae subsp. damselae corrig.15633VDA_002681diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Planctomyces brasiliensis103401Plabr_2819diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino)uracil reductase
Prochlorococcus marinus subsp. marinusPro_1339Pyrimidine reductase
Proteus mirabilis105697HMPREF0693_3369riboflavin biosynthesis protein RibD
Providencia alcalifaciens105687PROVALCAL_00198riboflavin biosynthesis protein RibD
Pseudomonas putida100650PP_0514riboflavin biosynthesis protein RibD
Pseudomonas stutzeri14165PSTAB_0722riboflavin biosynthesis protein RibD
Rahnella aquatilis105701Rahaq2_3456riboflavin biosynthesis protein RibD
Rhodobacter sphaeroides12203RSP_0393diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase
Roseobacter denitrificans15277RD1_1799riboflavin biosynthesis protein ribD
Roseobacter litoralis15278RLO149_c029190riboflavin biosynthesis protein RibD
Saccharopolyspora erythraea13426SACE_2887riboflavin-specific deaminase
Salinispora tropica105044Strop_18745-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase
Selenomonas ruminantium subsp. lactilytica103574SELR_09850putative 5-amino-6-(5-phosphoribosylamino) uracil reductase / diaminohydroxyphosphoribosylaminopyrimi dine deaminase
Serratia odorifera102598HMPREF0758_0227riboflavin biosynthesis protein RibD
Shimwellia blattae105725EB105725_34_00330diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Sporichthya polymorpha12702Spopo_31_16930Putative riboflavin/cytosine deaminase
Streptomyces cattleya14057SCAT_5370fused diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino) uracil reductase
Streptomyces clavuligerus13307SCLAV_0681putative riboflavin/cytosine deaminase
Streptomyces mobaraensis13819H340_26746riboflavin biosynthesis protein RibD
Streptomyces pristinaespiralis13074SSDG_03622riboflavin biosynthesis protein RibD
Streptomyces purpureus13925STRPU_03_00830Riboflavin biosynthesis protein RibD
Streptomyces venezuelae13096SVEN_1041Diaminohydroxyphosphoribosylaminopyrimidine deaminase or 5-amino-6-(5-phosphoribosylamino)uracil reductase
Streptosporangium roseum3776Sros_2832Diaminohydroxyphosphoribosylaminopyrimidinedeami nase
Synechococcus elongatusSynpcc7942_02035-amino-6-(5-phosphoribosylamino)uracil reductase / diaminohydroxyphosphoribosylaminopyrimidine deaminase
Synechocystis sp.slr0066riboflavin biosynthesis protein
Thauera linaloolentis102519C666_18485riboflavin biosynthesis protein RibD
Thermanaerovibrio acidaminovoransTaci_1010riboflavin biosynthesis protein RibD
Thermobispora bispora14880Tbis_1371riboflavin biosynthesis protein RibD
Thermodesulfobium narugense100082Thena_1001riboflavin biosynthesis protein RibD
Thermodesulfovibrio yellowstoniiTHEYE_A1298riboflavin biosynthesis protein RibD
Thermomicrobium roseumtrd_0502riboflavin biosynthesis protein RibD
Thermotoga thermarum107925Theth_1643diaminohydroxyphosphoribosylaminopyrimidine deaminase; 5-amino-6-(5-phosphoribosylamino)uracil reductase
Thermus thermophilus101084TTHA1064diaminohydroxyphosphoriboxylaminopyrimidine deaminase + 5-amino-6-(5-phosphoribosylamino)uracil reductase (RibD)
Thermus thermophilus101085TT_C0699diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductase
Vibrio alginolyticus15630N646_2832riboflavin-specific deaminase
Vibrio ichthyoenteri15847VII00023_02619riboflavin-specific deaminase
Vibrio metschnikovii103153VIB_000655diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase
Vibrio orientalis15638VIOR3934_14132diaminohydroxyphosphoribosylaminopyrimidine deaminase
Vibrio tubiashii15644VITU9109_06230diaminohydroxyphosphoribosylaminopyrimidine deaminase
Vibrio vulnificus15645B736_09070diaminohydroxyphosphoribosylaminopyrimidine deaminase
Xenococcus sp.Xen7305DRAFT_00021960diaminohydroxyphosphoribosylaminopyrimidine deaminase
Yersinia bercovieri105717yberc0001_141605-amino-6-(5-phosphoribosylamino)uracil reductase
Yersinia rohdei105715yrohd0001_25505-amino-6-(5-phosphoribosylamino)uracil reductase