THIC_RHILO
ID THIC_RHILO Reviewed; 619 AA.
AC Q98AZ3; Q8KJ38;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Phosphomethylpyrimidine synthase {ECO:0000255|HAMAP-Rule:MF_00089};
DE EC=4.1.99.17 {ECO:0000255|HAMAP-Rule:MF_00089};
DE AltName: Full=Hydroxymethylpyrimidine phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00089};
DE Short=HMP-P synthase {ECO:0000255|HAMAP-Rule:MF_00089};
DE Short=HMP-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00089};
DE Short=HMPP synthase {ECO:0000255|HAMAP-Rule:MF_00089};
DE AltName: Full=Thiamine biosynthesis protein ThiC {ECO:0000255|HAMAP-Rule:MF_00089};
GN Name=thiC {ECO:0000255|HAMAP-Rule:MF_00089}; OrderedLocusNames=mll5795;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=R7A;
RX PubMed=12003951; DOI=10.1128/jb.184.11.3086-3095.2002;
RA Sullivan J.T., Trzebiatowski J.R., Cruickshank R.W., Gouzy J., Brown S.D.,
RA Elliot R.M., Fleetwood D.J., McCallum N.G., Rossbach U., Stuart G.S.,
RA Weaver J.E., Webby R.J., de Bruijn F.J., Ronson C.W.;
RT "Comparative sequence analysis of the symbiosis island of Mesorhizobium
RT loti strain R7A.";
RL J. Bacteriol. 184:3086-3095(2002).
CC -!- FUNCTION: Catalyzes the synthesis of the hydroxymethylpyrimidine
CC phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR)
CC in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.
CC {ECO:0000255|HAMAP-Rule:MF_00089}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L-
CC methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'-
CC deoxyadenosine + CO + formate + 3 H(+) + L-methionine;
CC Xref=Rhea:RHEA:24840, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
CC ChEBI:CHEBI:17245, ChEBI:CHEBI:17319, ChEBI:CHEBI:57844,
CC ChEBI:CHEBI:58354, ChEBI:CHEBI:59789, ChEBI:CHEBI:137981;
CC EC=4.1.99.17; Evidence={ECO:0000255|HAMAP-Rule:MF_00089};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00089};
CC Note=Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated
CC with 3 cysteines and an exchangeable S-adenosyl-L-methionine.
CC {ECO:0000255|HAMAP-Rule:MF_00089};
CC -!- PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_00089}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00089}.
CC -!- SIMILARITY: Belongs to the ThiC family. {ECO:0000255|HAMAP-
CC Rule:MF_00089}.
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DR EMBL; BA000012; BAB52179.1; -; Genomic_DNA.
DR EMBL; AL672115; CAD31245.1; -; Genomic_DNA.
DR AlphaFoldDB; Q98AZ3; -.
DR SMR; Q98AZ3; -.
DR STRING; 266835.14025579; -.
DR EnsemblBacteria; BAB52179; BAB52179; BAB52179.
DR KEGG; mlo:mll5795; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_5; -.
DR OMA; TWELFRD; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0016830; F:carbon-carbon lyase activity; IEA:InterPro.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0009229; P:thiamine diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.20.20.540; -; 1.
DR HAMAP; MF_00089; ThiC; 1.
DR InterPro; IPR037509; ThiC.
DR InterPro; IPR025747; ThiC-associated_dom.
DR InterPro; IPR038521; ThiC/Bza_core_dom.
DR InterPro; IPR002817; ThiC/BzaA/B.
DR PANTHER; PTHR30557; PTHR30557; 1.
DR Pfam; PF13667; ThiC-associated; 1.
DR Pfam; PF01964; ThiC_Rad_SAM; 1.
DR SFLD; SFLDF00407; phosphomethylpyrimidine_syntha; 1.
DR TIGRFAMs; TIGR00190; thiC; 1.
PE 3: Inferred from homology;
KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; S-adenosyl-L-methionine;
KW Thiamine biosynthesis; Zinc.
FT CHAIN 1..619
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152830"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..17
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 220
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 249
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 278
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 314
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 334..336
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 375..378
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 414
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 418
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 441
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 482
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 562
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 565
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 570
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /ligand_note="4Fe-4S-S-AdoMet"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT CONFLICT 8
FT /note="T -> K (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 36..38
FT /note="QIR -> HIK (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 68
FT /note="T -> I (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 75
FT /note="K -> N (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 82
FT /note="H -> N (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 108
FT /note="V -> T (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 117..118
FT /note="PV -> LT (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 126..127
FT /note="RS -> KQ (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 163..165
FT /note="TLQ -> KLE (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 174
FT /note="S -> A (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 178
FT /note="L -> F (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 190
FT /note="H -> R (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 262
FT /note="D -> E (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 285
FT /note="G -> N (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 317
FT /note="V -> M (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 346
FT /note="H -> Q (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 360
FT /note="V -> I (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 402
FT /note="K -> Q (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 426
FT /note="A -> E (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 558
FT /note="L -> V (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 596
FT /note="E -> A (in Ref. 2; CAD31245)"
FT /evidence="ECO:0000305"
FT CONFLICT 605..618
FT /note="EESGAPLMPEAHEL -> DKTGVALMTGAPEP (in Ref. 2)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 619 AA; 68301 MW; DEAD6C9E8358ED4D CRC64;
MHEQRSLTMN ALTPAVSTGP LPASRKIHKS GVLHPQIRVP MREISVHPTA GEPPVIVYDP
SGPYTDPTVE TSIEKGLARL RHEWITARGD VEAYDGRHVR PEDNGFAVGE RLTPEFPVRN
RPLRARSGKA VTQLAYARAG IITPEMEFVA IRENLGREML RGTLQRDGEA FGASIPDLVT
PEFVRDEVAH GRAIIPANIN HPESEPMIIG RNFLVKINAN IGNSAVTSSM AEEVEKMVWA
IRWGADTVMD LSTGRNIHNI RDWIVRNAPV PIGTVPLYQA LEKVGGIAED LTWEVYRDTL
IEQAEQGVDY FTIHAGVRLH YIPLTVDRVT GIVSRGGSIM AKWCLHHHRE SFLYEHFAEV
CDICRAYDVS FSLGDGLRPG SIADANDAAQ FAELETLGEL TKIAWAKDCQ VMIEGPGHVP
MHKIKANMDK QLAVCGEAPF YTLGPLTTDI APGYDHITSG IGAAMIGWFG TAMLCYVTPK
EHLGLPDRND VKIGVITYKI AAHAADLAKG HPAAKVRDDA LSRARFEFRW EDQFNLSLDP
ETARSFHDQT LPKEAHKLAH FCSMCGPKFC SMRISHDIRA EAQKEGMAAM AAKYREGGDL
YVPAEESGAP LMPEAHELS
