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Protein

Phosphomethylpyrimidine synthase

Gene

thiC

Organism
Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction.1 Publication

Catalytic activityi

5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-(phosphomethyl)pyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO.2 Publications

Cofactori

[4Fe-4S] cluster2 PublicationsNote: Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.2 Publications

Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in the pathway thiamine diphosphate biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway thiamine diphosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei219SubstrateCombined sources1 Publication1
Binding sitei248SubstrateCombined sources1 Publication1
Binding sitei277SubstrateCombined sources1 Publication1
Binding sitei313SubstrateCombined sources1 Publication1
Binding sitei413SubstrateCombined sources1 Publication1
Metal bindingi417Zinc; via tele nitrogenCombined sources1 Publication1
Binding sitei440SubstrateCombined sources1 Publication1
Metal bindingi481Zinc; via tele nitrogenCombined sources1 Publication1
Metal bindingi561Iron-sulfur (4Fe-4S-S-AdoMet)Combined sources1 Publication1
Metal bindingi564Iron-sulfur (4Fe-4S-S-AdoMet)Combined sources1 Publication1
Metal bindingi569Iron-sulfur (4Fe-4S-S-AdoMet)Combined sources1 Publication1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionLyase
Biological processThiamine biosynthesis
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

BioCyciCAULO:CC2029-MONOMER
MetaCyc:MONOMER-14897
BRENDAi4.1.99.17 1218
UniPathwayiUPA00060

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphomethylpyrimidine synthase (EC:4.1.99.172 Publications)
Alternative name(s):
Hydroxymethylpyrimidine phosphate synthase
Short name:
HMP-P synthase
Short name:
HMP-phosphate synthase
Short name:
HMPP synthase
Thiamine biosynthesis protein ThiC
Gene namesi
Name:thiC
Ordered Locus Names:CC_2029
OrganismiCaulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)
Taxonomic identifieri190650 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
Proteomesi
  • UP000001816 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi417H → A: 5-fold reduction in catalytic activity. 1 Publication1
Mutagenesisi481H → A: 5-fold reduction in catalytic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001527931 – 612Phosphomethylpyrimidine synthaseAdd BLAST612

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi190650.CC_2029

Structurei

Secondary structure

1612
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 13Combined sources8
Beta strandi23 – 28Combined sources6
Beta strandi30 – 32Combined sources3
Beta strandi36 – 42Combined sources7
Helixi46 – 48Combined sources3
Beta strandi53 – 55Combined sources3
Helixi60 – 63Combined sources4
Turni71 – 73Combined sources3
Helixi80 – 85Combined sources6
Beta strandi89 – 91Combined sources3
Helixi100 – 103Combined sources4
Helixi108 – 110Combined sources3
Beta strandi123 – 125Combined sources3
Helixi133 – 138Combined sources6
Helixi144 – 154Combined sources11
Beta strandi159 – 161Combined sources3
Helixi180 – 188Combined sources9
Beta strandi191 – 193Combined sources3
Beta strandi215 – 220Combined sources6
Helixi229 – 241Combined sources13
Beta strandi245 – 249Combined sources5
Beta strandi253 – 255Combined sources3
Helixi256 – 264Combined sources9
Beta strandi271 – 273Combined sources3
Helixi275 – 282Combined sources8
Turni283 – 285Combined sources3
Helixi287 – 289Combined sources3
Helixi292 – 305Combined sources14
Beta strandi309 – 312Combined sources4
Helixi318 – 324Combined sources7
Beta strandi327 – 329Combined sources3
Helixi334 – 346Combined sources13
Helixi351 – 354Combined sources4
Helixi356 – 363Combined sources8
Turni364 – 367Combined sources4
Beta strandi369 – 372Combined sources4
Helixi381 – 383Combined sources3
Helixi387 – 405Combined sources19
Beta strandi410 – 413Combined sources4
Helixi420 – 422Combined sources3
Helixi423 – 433Combined sources11
Turni434 – 436Combined sources3
Beta strandi439 – 442Combined sources4
Helixi454 – 468Combined sources15
Beta strandi472 – 474Combined sources3
Turni478 – 482Combined sources5
Helixi487 – 508Combined sources22
Helixi513 – 525Combined sources13
Helixi529 – 534Combined sources6
Beta strandi535 – 538Combined sources4
Helixi539 – 545Combined sources7
Beta strandi548 – 550Combined sources3
Beta strandi557 – 559Combined sources3
Helixi560 – 563Combined sources4
Helixi568 – 576Combined sources9
Turni580 – 583Combined sources4
Helixi590 – 602Combined sources13
Beta strandi607 – 610Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EPMX-ray2.79A/B1-612[»]
3EPNX-ray2.11A/B1-612[»]
3EPOX-ray2.10A/B1-612[»]
4S2AX-ray2.93A1-612[»]
ProteinModelPortaliQ9A6Q5
SMRiQ9A6Q5
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9A6Q5

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni333 – 335Substrate bindingCombined sources1 Publication3
Regioni374 – 377Substrate bindingCombined sources1 Publication4

Sequence similaritiesi

Belongs to the ThiC family.Curated

Phylogenomic databases

eggNOGiENOG4105CBF Bacteria
COG0422 LUCA
HOGENOMiHOG000224484
KOiK03147
OMAiTWELFRD

Family and domain databases

Gene3Di3.20.20.540, 1 hit
HAMAPiMF_00089 ThiC, 1 hit
InterProiView protein in InterPro
IPR037509 ThiC
IPR025747 ThiC-associated_dom
IPR038521 ThiC/Bza_sf
IPR002817 ThiC/BzaA/B
PANTHERiPTHR30557 PTHR30557, 1 hit
PfamiView protein in Pfam
PF13667 ThiC-associated, 1 hit
PF01964 ThiC_Rad_SAM, 1 hit
SFLDiSFLDF00407 phosphomethylpyrimidine_syntha, 1 hit
TIGRFAMsiTIGR00190 thiC, 1 hit

Sequencei

Sequence statusi: Complete.

Q9A6Q5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNIQSTIKAV AETISTGPIP GSRKVYQAGE LFPELRVPFR EVAVHPSANE
60 70 80 90 100
PPVTIYDPSG PYSDPAIQID IEKGLPRTRE ALVVARGDVE EVADPRQVKP
110 120 130 140 150
EDNGFAQGKH LAPEFPDTGR KIYRAKPGKL VTQLEYARAG IITAEMEYVA
160 170 180 190 200
IRENLRREQD RPCVRDGEDF GASIPDFVTP EFVRQEIARG RAIIPANINH
210 220 230 240 250
GELEPMAIGR NFLVKINANI GNSAVLSTVA DEVDKLVWAT RWGADTVMDL
260 270 280 290 300
STGRNIHNIR DWIIRNSSVP IGTVPIYQAL EKVNGVAEDL NWEVFRDTLI
310 320 330 340 350
EQCEQGVDYF TIHAGVRLPF IPMTAKRVTG IVSRGGSIMA KWCLAHHKEN
360 370 380 390 400
FLYERFDEIC EIMRAYDVSF SLGDGLRPGS TADANDEAQF SELRTLGELT
410 420 430 440 450
KVAWKHGVQV MIEGPGHVAM HKIKANMDEQ LKHCHEAPFY TLGPLTTDIA
460 470 480 490 500
PGYDHITSAI GAAMIGWFGT AMLCYVTPKE HLGLPDRDDV KTGVITYKLA
510 520 530 540 550
AHAADLAKGH PGAAMWDDAI SRARFEFRWE DQFNLGLDPE TARKFHDETL
560 570 580 590 600
PKEAHKTAHF CSMCGPKFCS MKISQEVRDF AAGKAPNSAE LGMAEMSEKF
610
REQGSEIYLK TE
Length:612
Mass (Da):67,968
Last modified:June 1, 2001 - v1
Checksum:i59FB0AFB55668816
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005673 Genomic DNA Translation: AAK24004.1
PIRiH87500
RefSeqiNP_420836.1, NC_002696.2
WP_010919895.1, NC_002696.2

Genome annotation databases

EnsemblBacteriaiAAK24004; AAK24004; CC_2029
GeneIDi942808
KEGGiccr:CC_2029
PATRICifig|190650.5.peg.2049

Similar proteinsi

Entry informationi

Entry nameiTHIC_CAUVC
AccessioniPrimary (citable) accession number: Q9A6Q5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: June 1, 2001
Last modified: March 28, 2018
This is version 96 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health