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Protein

Phosphomethylpyrimidine synthase

Gene

thiC

Organism
Caulobacter crescentus (strain ATCC 19089 / CB15)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei219 – 2191Substrate
Binding sitei248 – 2481Substrate
Binding sitei277 – 2771Substrate
Binding sitei313 – 3131Substrate
Binding sitei413 – 4131Substrate
Metal bindingi417 – 4171Zinc
Binding sitei440 – 4401Substrate
Metal bindingi481 – 4811Zinc
Metal bindingi561 – 5611Iron-sulfur (4Fe-4S-S-AdoMet)
Metal bindingi564 – 5641Iron-sulfur (4Fe-4S-S-AdoMet)
Metal bindingi569 – 5691Iron-sulfur (4Fe-4S-S-AdoMet)

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Thiamine biosynthesis

Keywords - Ligandi

4Fe-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 crescentus (strain ATCC 19089 / CB15)
Taxonomic identifieri190650 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaCaulobacteralesCaulobacteraceaeCaulobacter
Proteomesi
  • UP000001816 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 612612Phosphomethylpyrimidine synthasePRO_0000152793Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi190650.CC_2029.

Structurei

Secondary structure

1
612
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 138Combined sources
Beta strandi23 – 286Combined sources
Beta strandi30 – 323Combined sources
Beta strandi36 – 427Combined sources
Helixi46 – 483Combined sources
Beta strandi53 – 553Combined sources
Helixi60 – 634Combined sources
Turni71 – 733Combined sources
Helixi80 – 856Combined sources
Beta strandi89 – 913Combined sources
Helixi100 – 1034Combined sources
Helixi108 – 1103Combined sources
Beta strandi123 – 1253Combined sources
Helixi133 – 1386Combined sources
Helixi144 – 15411Combined sources
Beta strandi159 – 1613Combined sources
Helixi180 – 1889Combined sources
Beta strandi191 – 1933Combined sources
Beta strandi215 – 2206Combined sources
Helixi229 – 24113Combined sources
Beta strandi245 – 2495Combined sources
Beta strandi253 – 2553Combined sources
Helixi256 – 2649Combined sources
Beta strandi271 – 2733Combined sources
Helixi275 – 2828Combined sources
Turni283 – 2853Combined sources
Helixi287 – 2893Combined sources
Helixi292 – 30514Combined sources
Beta strandi309 – 3124Combined sources
Helixi318 – 3247Combined sources
Beta strandi327 – 3293Combined sources
Helixi334 – 34613Combined sources
Helixi351 – 3544Combined sources
Helixi356 – 3638Combined sources
Turni364 – 3674Combined sources
Beta strandi369 – 3724Combined sources
Helixi381 – 3833Combined sources
Helixi387 – 40519Combined sources
Beta strandi410 – 4134Combined sources
Helixi420 – 4223Combined sources
Helixi423 – 43311Combined sources
Turni434 – 4363Combined sources
Beta strandi439 – 4424Combined sources
Helixi454 – 46815Combined sources
Beta strandi472 – 4743Combined sources
Turni478 – 4825Combined sources
Helixi487 – 50822Combined sources
Helixi513 – 52513Combined sources
Helixi529 – 5346Combined sources
Beta strandi535 – 5384Combined sources
Helixi539 – 5457Combined sources
Beta strandi548 – 5503Combined sources
Beta strandi557 – 5593Combined sources
Helixi560 – 5634Combined sources
Helixi568 – 5769Combined sources
Turni580 – 5834Combined sources
Helixi590 – 60213Combined sources
Beta strandi607 – 6104Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EPMX-ray2.79A/B1-612[»]
3EPNX-ray2.11A/B1-612[»]
3EPOX-ray2.10A/B1-612[»]
4S2AX-ray2.93A1-612[»]
ProteinModelPortaliQ9A6Q5.
SMRiQ9A6Q5. Positions 15-612.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9A6Q5.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni333 – 3353Substrate binding
Regioni374 – 3774Substrate binding

Sequence similaritiesi

Belongs to the ThiC family.Curated

Phylogenomic databases

eggNOGiENOG4105CBF. Bacteria.
COG0422. LUCA.
HOGENOMiHOG000224484.
KOiK03147.
OMAiTWELFRD.
OrthoDBiEOG6NWBM5.

Family and domain databases

HAMAPiMF_00089. ThiC.
InterProiIPR002817. ThiC.
IPR025747. ThiC-associated_dom.
[Graphical view]
PfamiPF13667. ThiC-associated. 1 hit.
PF01964. ThiC_Rad_SAM. 1 hit.
[Graphical view]
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.
PATRICi21301076. VBICauCre124313_2049.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3EPMX-ray2.79A/B1-612[»]
3EPNX-ray2.11A/B1-612[»]
3EPOX-ray2.10A/B1-612[»]
4S2AX-ray2.93A1-612[»]
ProteinModelPortaliQ9A6Q5.
SMRiQ9A6Q5. Positions 15-612.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi190650.CC_2029.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK24004; AAK24004; CC_2029.
GeneIDi942808.
KEGGiccr:CC_2029.
PATRICi21301076. VBICauCre124313_2049.

Phylogenomic databases

eggNOGiENOG4105CBF. Bacteria.
COG0422. LUCA.
HOGENOMiHOG000224484.
KOiK03147.
OMAiTWELFRD.
OrthoDBiEOG6NWBM5.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ9A6Q5.

Family and domain databases

HAMAPiMF_00089. ThiC.
InterProiIPR002817. ThiC.
IPR025747. ThiC-associated_dom.
[Graphical view]
PfamiPF13667. ThiC-associated. 1 hit.
PF01964. ThiC_Rad_SAM. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00190. thiC. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 19089 / CB15.
  2. "A 'radical dance' in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase."
    Chatterjee A., Hazra A.B., Abdelwahed S., Hilmey D.G., Begley T.P.
    Angew. Chem. Int. Ed. 49:8653-8656(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: CATALYTIC ACTIVITY, REACTION MECHANISM.
  3. "Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily."
    Chatterjee A., Li Y., Zhang Y., Grove T.L., Lee M., Krebs C., Booker S.J., Begley T.P., Ealick S.E.
    Nat. Chem. Biol. 4:758-765(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEXES WITH SUBSTRATE AND ZINC, FUNCTION, CATALYTIC ACTIVITY, EPR SPECTROSCOPY, MOSSBAUER SPECTROSCOPY, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiTHIC_CAUCR
AccessioniPrimary (citable) accession number: Q9A6Q5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: June 1, 2001
Last modified: February 17, 2016
This is version 84 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.