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Rule : ATP-dependent dethiobiotin synthetase BioD (BIOD)

Rule Description

ID NRULE_0184
Rule name BIOD
Created 2013-03-27
Protein name
Protein name
Full
ATP-dependent dethiobiotin synthetase BioD
EC
EC 6.3.3.3
Synonym
Full
DTB synthetase
Dethiobiotin synthase
Short
DTBS
Gene name bioD
Rule Trigger HAMAP; MF_00336; hit=1
OR
TIGRFAMs; TIGR00347; hit=1
Cross Reference
Gene Ontology
GO
GO:0005737, C:cytoplasm, IEA:UniProtKB-SubCell
GO:0005524, F:ATP binding, IEA:UniProtKB-KW
GO:0004141, F:dethiobiotin synthase activity, IDA:UniProtKB
GO:0000287, F:magnesium ion binding, IEA:InterPro
GO:0009102, P:biotin biosynthetic process, IMP:EcoCyc
Enzyme and pathway databases
UniPathway
UPA00078, UER00161
Family and domain databases
HAMAP
MF_00336, BioD, 1, -
InterPro
IPR004472, DTB_synth_BioD
Pfam
PF01656, CbiA, 1
PIRSF
PIRSF006755, DTB_synth, 1
TIGRFAMs
TIGR00347, bioD, 1
Feature
P13000 Escherichia coli (strain K12).
NP_BIND13 - 18ATP.
NP_BIND116 - 119ATP.
NP_BIND176 - 177ATP.
NP_BIND205 - 207ATP.
METAL13Magnesium 1.
METAL17Magnesium 2.
METAL55Magnesium 2.
METAL116Magnesium 2.
BINDING42Substrate.
BINDING55ATP.
BINDING212ATP.
P22818 Lysinibacillus sphaericus (Bacillus sphaericus).
NP_BIND115 - 118ATP (By similarity).
METAL12Magnesium 1 (By similarity).
METAL16Magnesium 2 (By similarity).
METAL54Magnesium 2 (By similarity).
METAL115Magnesium 2 (By similarity).
BINDING41Substrate (By similarity).
BINDING54ATP (By similarity).
BINDING234ATP (By similarity).
General annotation
Function
Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring (By similarity)
Catalytic activity
ATP + 7,8-diaminononanoate + CO(2) = ADP + phosphate + dethiobiotin
Cofactor
Magnesium (By similarity)
Pathway
Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2
Sequence similarities
Belongs to the dethiobiotin synthetase family
Reference
P13000 Escherichia coli (strain K12).
3058702
The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. (J Biol Chem. 1988)
4892372
Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12. (J Bacteriol. 1969)
4921568
The purification and properties of dethiobiotin synthetase. (J Biol Chem. 1970)
P22818 Lysinibacillus sphaericus (Bacillus sphaericus).
2110099
Cloning and characterization of the Bacillus sphaericus genes controlling the bioconversion of pimelate into dethiobiotin. (Gene. 1990)



Related Function

Function name
Biotin biosynthesis

CDS

Data Download
Scientific name NBRC No. CDS Product name
Acaryochloris marina102967AM1_2626dethiobiotin synthetase
Acetobacter aceti14818AaceN1_010100008202dethiobiotin synthase
Acetobacter pasteurianus105190APA32_10930Biotin synthesis protein
Acetobacter pasteurianus101655APT_0467biotin synthesis protein
Acetobacter tropicalis101654ATPR_2404biotin synthesis protein
Acidiphilium multivorum100883ACMV_21080dethiobiotin synthetase
Acidithiobacillus ferrooxidansLferr_0422dethiobiotin synthase
Lferr_1373dethiobiotin synthase
Acinetobacter radioresistens102413ACRAD_30_00210ATP-dependent dethiobiotin synthetase BioD
Acinetobacter sp.100985ACT4_021_01620ATP-dependent dethiobiotin synthetase BioD
Actinoalloteichus cyanogriseus14455G443_05_02680dethiobiotin synthetase
Actinoalloteichus spitiensis102582ACTIDRAF_08180hypothetical protein
Actinomadura atramentaria14695G339_21975dithiobiotin synthetase
Actinoplanes missouriensis102363AMIS_68010putative dethiobiotin synthetase
Actinosynnema mirum14064Amir_5739dethiobiotin synthase
Alicyclobacillus acidocaldarius subsp. acidocaldarius15652Aaci_2855dethiobiotin synthase
Alteromonas macleodii102226MASE_06290cobyrinic acid a,c-diamide synthase:dethiobiotin synthase
Amycolatopsis azurea14573C791_1412Dethiobiotin synthetase
Amycolatopsis mediterranei13415RAM_11290dethiobiotin synthetase
Anoxybacillus flavithermus15317Aflv_1070Dethiobiotin synthetase
Aquifex aeolicusaq_557dethiobiotin synthetase
Aquimarina agarilytica107695AagaZ_020100005630dethiobiotin synthetase
Arthrobacter globiformis12137ARGLB_033_00080ATP-dependent dethiobiotin synthetase BioD
Austwickia chelonae105200AUCHE_22_00450ATP-dependent dethiobiotin synthetase BioD
Bacillus amyloliquefaciens15535BAMF_1921dethiobiotin synthetase
Bacillus atrophaeus13721BATRMS_05_00790dithiobiotin synthetase
Bacillus cereus15305BC_4118Dethiobiotin synthetase
Bacillus licheniformis12200BL00955dethiobiotin synthetase
Bacillus licheniformis12195BLi00769dethiobiotin synthase BioD
Bacillus mojavensis15718GYU_01_00460dithiobiotin synthetase
Bacillus mycoides101228bmyco0001_37450Dethiobiotin synthetase
Bacillus pseudomycoides101232bpmyx0001_36010Dethiobiotin synthetase
Bacillus subtilis3134BSU6633_12882dithiobiotin synthetase
Bacillus subtilis subsp. subtilis13719BSU30210dethiobiotin synthetase
Bacillus thuringiensis101235bthur0008_39110Dethiobiotin synthetase
Bacillus vallismortis101236BvalD_010100010250dithiobiotin synthetase
Bacteroides vulgatus14291BVU_2783dethiobiotin synthetase
Balneola vulgarisB155_RS0102010dethiobiotin synthase
Bradyrhizobium diazoefficiens14792blr2098dethiobiotin synthase
Brevibacillus brevis100599BBR47_54630dethiobiotin synthetase
Brevibacterium linens12170BlinB_010200019305dethiobiotin synthase
Brevundimonas subvibrioides16000Bresu_2821dethiobiotin synthase
Calditerrivibrio nitroreducens101217Calni_1371dethiobiotin synthase
Candidatus Nitrosopumilus sp.NSED_04545dethiobiotin synthase
Catenulispora acidiphila102108Caci_7723dethiobiotin synthase
Caulobacter segnis15250Cseg_2628dethiobiotin synthase
Cellulophaga lytica14961Celly_1037Dethiobiotin synthetase
Cenarchaeum symbiosumCENSYa_0979cobyrinic acid a,c-diamide synthase/dethiobiotin synthetase
Chitinispirillum alkaliphilumCHISP_2156Dethiobiotin synthetase
Chitinivibrio alkaliphilusCALK_0181dithiobiotin synthetase
Chitinophaga pinensis15968Cpin_3668dethiobiotin synthase
Chloracidobacterium thermophilum BCabther_A0525dethiobiotin synthase
Chlorobaculum tepidum103806CT0048dethiobiotin synthase
Chlorobium limicola103803Clim_2426dethiobiotin synthase
Chromobacterium violaceum12614CV_0598dethiobiotin synthase
Chryseobacterium gleum15054HMPREF0204_13793dethiobiotin synthase
Chthoniobacter flavusCfE428DRAFT_3033dethiobiotin synthase
Clostridium acetobutylicum13948CA_C1361Dethiobiotin synthetase
Clostridium kluyveri12016CKR_0850hypothetical protein
Clostridium thermocellum103400Cthe_0021dethiobiotin synthase
Conexibacter woesei100937Cwoe_1568dethiobiotin synthase
Coprobacillus sp.HMPREF1021_02309dethiobiotin synthase
Coraliomargarita akajimensisCaka_0766aminotransferase class I and II
Corynebacterium efficiens100395CE1420dethiobiotin synthase
Corynebacterium glutamicum12168Cgl2605Dethiobiotin synthetase
Corynebacterium glutamicum12153KIQ_12710dithiobiotin synthetase
Corynebacterium striatum15291HMPREF0308_2401dethiobiotin synthase
Cupriavidus metallidurans102507Rmet_0116dethiobiotin synthetase
Cystobacter fuscus100088D187_000312Dethiobiotin synthetase
Cytophaga hutchinsonii15051CHU_2977dethiobiotin synthetase
Deferribacter desulfuricans101012DEFDS_1298dethiobiotin synthetase
Desulfovibrio magneticus104933DMR_18990dethiobiotin synthetase
Desulfovibrio vulgaris subsp. vulgaris104121DVU_2565dethiobiotin synthetase
Edwardsiella tarda105688ET1_05_02380dethiobiotin synthetase BioD2
ET1_08_00200dethiobiotin synthetase BioD1
Enterobacter aerogenes13534EAE_14460dithiobiotin synthetase
EAE_18360putative dithiobiotin synthetase
Enterobacter cloacae subsp. cloacae13535ECL_02219putative dithiobiotin synthetase
ECL_02958dithiobiotin synthetase
Enterobacter hormaechei105718HMPREF9086_0368dethiobiotin synthetase
HMPREF9086_1082dethiobiotin synthetase
Enterococcus hirae3181EHR_07050dethiobiotin synthetase
Escherichia coli3972EcolC_2037dethiobiotin synthase
EcolC_2865dethiobiotin synthase
Escherichia coli13500WFL_04040dithiobiotin synthetase
WFL_08610putative dithiobiotin synthetase
Escherichia coli12713Y75_0755dethiobiotin synthetase
Y75_1589predicted dethiobiotin synthetase
Escherichia fergusonii102419EFER_1443putative synthase (similar to dethiobiotin synthetase)
EFER_2334dethiobiotin synthetase
Escherichia hermannii105704EH105704_05_02150ATP-dependent dethiobiotin synthetase BioD
EH105704_23_00110ATP-dependent dethiobiotin synthetase BioD
Fibrobacter succinogenesFisuc_2954dethiobiotin synthase
Fischerella sp.PCC9339_RS0132125dithiobiotin synthetase
Flavobacterium johnsoniae14942Fjoh_0811dethiobiotin synthase
Flexibacter litoralis15988Fleli_1938dethiobiotin synthase
Fluviicola taffensis106335Fluta_3297Dethiobiotin synthetase
Frateuria aurantia3245Fraau_0760dethiobiotin synthase
Fusobacterium nucleatum subsp. NucleatumFN1001Dethiobiotin synthetase
Gemmatimonas aurantiaca100505GAU_2842dethiobiotin synthetase
Gloeobacter violaceusgll3509dethiobiotin synthetase
Gluconacetobacter hansenii14816GXY_10229dethiobiotin synthase
Gluconobacter frateurii101659GfraN1_010100010264dethiobiotin synthetase BioD
Gordonia aichiensis108223GOACH_16_01190ATP-dependent dethiobiotin synthetase BioD
Gordonia alkanivorans16433GOALK_084_00120dethiobiotin synthetase
Gordonia amarae15530GOAMR_51_00030ATP-dependent dethiobiotin synthetase BioD
Gordonia amicalis100051GOAMI_54_00220ATP-dependent dethiobiotin synthetase BioD
Gordonia araii100433GOARA_052_00320ATP-dependent dethiobiotin synthetase BioD
Gordonia bronchialis16047Gbro_2973dethiobiotin synthase
Gordonia effusa100432GOEFS_065_00010ATP-dependent dethiobiotin synthetase BioD
Gordonia hirsuta16056GOHSU_02_00580ATP-dependent dethiobiotin synthetase BioD
Gordonia namibiensis108229GONAM_46_00230ATP-dependent dethiobiotin synthetase BioD
Gordonia otitidis100426GOOTI_099_00050ATP-dependent dethiobiotin synthetase BioD
Gordonia polyisoprenivorans16320GOPIP_071_00320ATP-dependent dethiobiotin synthetase BioD
Gordonia rhizosphera16068GORHZ_073_00150ATP-dependent dethiobiotin synthetase
Gordonia rubripertincta101908GORBP_068_00570ATP-dependent dethiobiotin synthetase BioD
Gordonia sihwensis108236GSI01S_06_02060ATP-dependent dethiobiotin synthetase BioD
Gordonia soli108243GS4_30_00640ATP-dependent dethiobiotin synthetase BioD
Gordonia sputi100414GOSPT_058_00900ATP-dependent dethiobiotin synthetase BioD
Gordonia terrae100016GOTRE_063_00250ATP-dependent dethiobiotin synthetase BioD
Haloarcula vallismortis14741C437_16096dethiobiotin synthase
Halomonas elongata15536HELO_2166dithiobiotin synthetase
Holophaga foetidaHOLFODRAFT_RS21420hypothetical protein
Hyphomonas neptunium14232HNE_1249dethiobiotin synthase
Intrasporangium calvum12989Intca_2346dethiobiotin synthase
Kitasatospora setae14216KSE_71100putative dethiobiotin synthetase
Klebsiella pneumoniae14438KPR_2736
KPR_3785
Klebsiella pneumoniae subsp. rhinoscleromatis105682HMPREF0484_1377dethiobiotin synthase
HMPREF0484_4209dethiobiotin synthase
Kocuria rhizophila103217KRH_02470dethiobiotin synthetase
Kordia algicida100336KAOT1_14932dethiobiotin synthetase
Kribbella flavida14399Kfla_6011dethiobiotin synthase
Kyrpidia tusciae15312Btus_2596dethiobiotin synthase
Lentisphaera araneosaLNTAR_23564dethiobiotin synthetase (bioD)
Leptospira interrogansLA_2141dethiobiotin synthetase
Leuconostoc mesenteroides subsp. cremoris107766HMPREF0555_0204dethiobiotin synthase
Leuconostoc mesenteroides subsp. mesenteroides100496LEUM_0304dethiobiotin synthase
Leuconostoc pseudomesenteroides107767LpseK3_010100013272dethiobiotin synthase
Magnetospirillum gryphiswaldense15271MGR_0753Dethiobiotin synthetase
Magnetospirillum magnetotacticum15272Magn03008477COG0132: Dethiobiotin synthetase
Marinomonas mediterranea103028Marme_3247Dethiobiotin synthetase
Mariprofundus ferrooxydansSPV1_10321Dethiobiotin synthase
Marivirga tractuosa15989Ftrac_1013dethiobiotin synthase
Methanocaldococcus jannaschii100440MJ_1299dethiobiotin synthetase (bioD)
Methanococcus maripaludis101832MMP1573Dethiobiotin synthetase
Methanococcus maripaludisMmarC5_0003dethiobiotin synthase
Methylobacterium radiotolerans15690Mrad2831_0738dethiobiotin synthase
Micromonospora aurantiaca16155Micau_1679dethiobiotin synthase
Microscilla marina16560M23134_00626dethiobiotin synthase
Mobilicoccus pelagius104925MOPEL_135_01420dethiobiotin synthetase
Niastella koreensis106392Niako_0916Dethiobiotin synthetase
Nitriliruptor alkaliphilusNitalDRAFT_4965dethiobiotin synthetase
Nitrosomonas europaea14298NE2296Cobyrinic acid a,c-diamide synthase:Dethiobiotin synthase
Nitrososphaera viennensisNVIE_004890dethiobiotin synthase
Nitrospina gracilisNITGR_950041Dethiobiotin synthetase
Nocardiopsis dassonvillei14626Ndas_0613dethiobiotin synthase
Nostoc sp.all4667 hypothetical protein
Ochrobactrum anthropi15819Oant_2821dethiobiotin synthase
Ochrobactrum intermedium15820OINT_2000088dethiobiotin synthase
Paenibacillus alvei3343PAV_1c04830ATP-dependent dethiobiotin synthetase BioD
Paenibacillus peoriae15541PpeoK3_010100015221dethiobiotin synthase
Pedobacter heparinus12017Phep_1910dethiobiotin synthase
Pedobacter saltans100064Pedsa_3336dethiobiotin synthase
Pelobacter carbinolicus103641Pcar_1459dethiobiotin synthetase
Pelobacter propionicus103807Ppro_1176dethiobiotin synthase
Phaeobacter gallaeciensis16654PGA1_c09140dethiobiotin synthetase BioD
Photobacterium damselae subsp. damselae corrig.15633VDA_002295dethiobiotin synthetase
Phycisphaera mikurensis102666PSMK_21420dethiobiotin synthetase
Planctomyces brasiliensis103401Plabr_3663Dethiobiotin synthetase
Prochlorococcus marinus subsp. marinusPro_1625Dethiobiotin synthetase
Propionibacterium avidum15671HMPREF9153_1992dethiobiotin synthetase
Proteus mirabilis105697HMPREF0693_0865dethiobiotin synthase
HMPREF0693_1959dethiobiotin synthase
Providencia alcalifaciens105687PROVALCAL_02856dethiobiotin synthase
PROVALCAL_03256dethiobiotin synthase
Pseudomonas putida100650PP_0366dethiobiotin synthetase
Pseudomonas stutzeri14165PSTAB_3813dithiobiotin synthetase
Rahnella aquatilis105701Rahaq2_2438dethiobiotin synthase
Rahaq2_3121dethiobiotin synthase
Renibacterium salmoninarum15589RSal33209_0562dethiobiotin synthetase
Rhizobium sp.101917NGR_c25120dethiobiotin synthetase BioD
Rhodobacter capsulatus16581RCAP_rcc03365dethiobiotin synthase
Rhodococcus erythropolis100887RER_35030dethiobiotin synthetase
Rhodococcus opacus108011ROP_07810dethiobiotin synthetase
Saccharomonospora azurea14651SacazDRAFT_03941dethiobiotin synthase
Saccharomonospora cyanea14841SaccyDRAFT_1257dethiobiotin synthase
Saccharomonospora glauca14831SacglDRAFT_01188dethiobiotin synthase
Saccharomonospora viridis12207Svir_10780dethiobiotin synthase
Saccharopolyspora erythraea13426SACE_0978dethiobiotin synthetase
Saccharopolyspora spinosa15153SspiN1_010100017371dethiobiotin synthase
Saccharothrix espanaensis15066BN6_68770Dethiobiotin synthetase
Salinispora tropica105044Strop_1571dethiobiotin synthase
Selenomonas ruminantium subsp. lactilytica103574SELR_19730putative dethiobiotin synthetase
Serratia odorifera102598HMPREF0758_3827dethiobiotin synthase
HMPREF0758_4795dethiobiotin synthase
Shimwellia blattae105725EB105725_03_00280ATP-dependent dethiobiotin synthetase BioD
EB105725_05_02200dethiobiotin synthetase BioD2
Solitalea canadensis15130Solca_1380dethiobiotin synthase
Sphingobacterium spiritivorum14948HMPREF0766_11939dethiobiotin synthase
Sphingobium japonicum101211SJA_C1-02720dethiobiotin synthase
Sphingobium sp.103272SLG_35150dethiobiotin synthetase
Sphingomonas echinoides15742SechA1_010100004868dithiobiotin synthetase
Sphingomonas wittichii105917Swit_1255dethiobiotin synthase
Sporichthya polymorpha12702Spopo_31_09500ATP-dependent dethiobiotin synthetase BioD
Stackebrandtia nassauensis102104Snas_0472dethiobiotin synthase
Staphylococcus epidermidis12993SE_0179dethiobiotin synthetase
Streptomyces avermitilis14893SAV7091putative dethiobiotin synthetase
Streptomyces cattleya14057SCAT_0349Dethiobiotin synthetase
SCAT_p1298Dethiobiotin synthetase
Streptomyces clavuligerus13307SCLAV_0533Dethiobiotin synthetase
Streptomyces ghanaensis15414SSFG_06091dithiobiotin synthetase
Streptomyces mobaraensis13819H340_16536dithiobiotin synthetase
Streptomyces pristinaespiralis13074SSDG_00912dithiobiotin synthetase
Streptomyces purpureus13925STRPU_02_00710ATP-dependent dethiobiotin synthetase BioD
Streptomyces sviceus13980SSEG_04945dethiobiotin synthase
Streptomyces venezuelae13096SVEN_0846Dethiobiotin synthetase
Streptosporangium roseum3776Sros_8310Dethiobiotin synthase
Synechococcus elongatusSynpcc7942_0030dethiobiotin synthase
Synechocystis sp.slr0523dethiobiotin synthetase; BioD
Thauera linaloolentis102519C666_07890dethiobiotin synthase
Thermanaerovibrio acidaminovoransTaci_0245dethiobiotin synthase
Thermodesulfobium narugense100082Thena_1826dethiobiotin synthase
Thermodesulfovibrio yellowstoniiTHEYE_A1875dethiobiotin synthase
Thermomonospora curvata15933Tcur_3699dethiobiotin synthase
Tsukamurella paurometabola16120Tpau_2000dethiobiotin synthase
Turicella otitidis106139HMPREF9719_00383dethiobiotin synthase
Vibrio alginolyticus15630N646_0167dithiobiotin synthetase
Vibrio ichthyoenteri15847VII00023_15136dithiobiotin synthetase
Vibrio metschnikovii103153VIB_001493dethiobiotin synthetase
Vibrio orientalis15638VIOR3934_03207dithiobiotin synthetase
Vibrio tubiashii15644VITU9109_16338dithiobiotin synthetase
Xenococcus sp.Xen7305DRAFT_00044530dethiobiotin synthase
Yersinia bercovieri105717yberc0001_27680Dethiobiotin synthetase
yberc0001_36840dethiobiotin synthetase YnfK
Yersinia rohdei105715yrohd0001_31690Dethiobiotin synthase
yrohd0001_36040Dethiobiotin synthetase
Zymomonas mobilis subsp. pomaceae13757Zymop_1205dethiobiotin synthase