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Protein

Phosphomethylpyrimidine synthase

Gene

thiC

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 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.2 Publications

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.UniRule annotation

Cofactori

[4Fe-4S] clusterUniRule annotationNote: Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine.UniRule annotation

Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in the pathway thiamine diphosphate biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
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 sitei239SubstrateUniRule annotation1
Binding sitei268SubstrateUniRule annotation1
Binding sitei297SubstrateUniRule annotation1
Binding sitei333SubstrateUniRule annotation1
Binding sitei433SubstrateUniRule annotation1
Metal bindingi437ZincUniRule annotation1
Binding sitei460SubstrateUniRule annotation1
Metal bindingi501ZincUniRule annotation1
Metal bindingi581Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1
Metal bindingi584Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1
Metal bindingi589Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation1

GO - Molecular functioni

GO - Biological processi

  • thiamine biosynthetic process Source: EcoCyc
  • thiamine diphosphate biosynthetic process Source: UniProtKB-UniPathway
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

BioCyciEcoCyc:THIC-MONOMER.
ECOL316407:JW3958-MONOMER.
MetaCyc:THIC-MONOMER.
UniPathwayiUPA00060.

Names & Taxonomyi

Protein namesi
Recommended name:
Phosphomethylpyrimidine synthaseUniRule annotation (EC:4.1.99.17UniRule annotation)
Alternative name(s):
Hydroxymethylpyrimidine phosphate synthaseUniRule annotation
Short name:
HMP-P synthaseUniRule annotation
Short name:
HMP-phosphate synthaseUniRule annotation
Short name:
HMPP synthaseUniRule annotation
Thiamine biosynthesis protein ThiCUniRule annotation
Gene namesi
Name:thiCUniRule annotation
Ordered Locus Names:b3994, JW3958
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11585. thiC.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001528041 – 631Phosphomethylpyrimidine synthaseAdd BLAST631

Proteomic databases

EPDiP30136.
PaxDbiP30136.
PRIDEiP30136.

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

BioGridi4259335. 8 interactors.
DIPiDIP-10982N.
IntActiP30136. 7 interactors.
STRINGi511145.b3994.

Structurei

3D structure databases

ProteinModelPortaliP30136.
SMRiP30136.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni353 – 355Substrate bindingUniRule annotation3
Regioni394 – 397Substrate bindingUniRule annotation4

Sequence similaritiesi

Belongs to the ThiC family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CBF. Bacteria.
COG0422. LUCA.
HOGENOMiHOG000224484.
InParanoidiP30136.
KOiK03147.
OMAiTWELFRD.
PhylomeDBiP30136.

Family and domain databases

HAMAPiMF_00089. ThiC. 1 hit.
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.

P30136-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSATKLTRRE QRARAQHFID TLEGTAFPNS KRIYITGTHP GVRVPMREIQ
60 70 80 90 100
LSPTLIGGSK EQPQYEENEA IPVYDTSGPY GDPQIAINVQ QGLAKLRQPW
110 120 130 140 150
IDARGDTEEL TVRSSDYTKA RLADDGLDEL RFSGVLTPKR AKAGRRVTQL
160 170 180 190 200
HYARQGIITP EMEFIAIREN MGRERIRSEV LRHQHPGMSF GAHLPENITA
210 220 230 240 250
EFVRDEVAAG RAIIPANINH PESEPMIIGR NFLVKVNANI GNSAVTSSIE
260 270 280 290 300
EEVEKLVWST RWGADTVMDL STGRYIHETR EWILRNSPVP IGTVPIYQAL
310 320 330 340 350
EKVNGIAEDL TWEAFRDTLL EQAEQGVDYF TIHAGVLLRY VPMTAKRLTG
360 370 380 390 400
IVSRGGSIMA KWCLSHHQEN FLYQHFREIC EICAAYDVSL SLGDGLRPGS
410 420 430 440 450
IQDANDEAQF AELHTLGELT KIAWEYDVQV MIEGPGHVPM QMIRRNMTEE
460 470 480 490 500
LEHCHEAPFY TLGPLTTDIA PGYDHFTSGI GAAMIGWFGC AMLCYVTPKE
510 520 530 540 550
HLGLPNKEDV KQGLITYKIA AHAADLAKGH PGAQIRDNAM SKARFEFRWE
560 570 580 590 600
DQFNLALDPF TARAYHDETL PQESGKVAHF CSMCGPKFCS MKISQEVRDY
610 620 630
AATQTIEMGM ADMSENFRAR GGEIYLRKEE A
Length:631
Mass (Da):70,850
Last modified:October 1, 1993 - v2
Checksum:i6F2105B4792CBA3F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti623 – 630EIYLRKEE → RNLP in AAB95616 (PubMed:8432721).Curated8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M88701 Genomic DNA. Translation: AAB95616.1.
U00006 Genomic DNA. Translation: AAC43092.1.
U00096 Genomic DNA. Translation: AAC76968.1.
AP009048 Genomic DNA. Translation: BAE77325.1.
PIRiE65206.
RefSeqiNP_418422.1. NC_000913.3.
WP_001276926.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76968; AAC76968; b3994.
BAE77325; BAE77325; BAE77325.
GeneIDi948492.
KEGGiecj:JW3958.
eco:b3994.
PATRICi32123511. VBIEscCol129921_4108.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M88701 Genomic DNA. Translation: AAB95616.1.
U00006 Genomic DNA. Translation: AAC43092.1.
U00096 Genomic DNA. Translation: AAC76968.1.
AP009048 Genomic DNA. Translation: BAE77325.1.
PIRiE65206.
RefSeqiNP_418422.1. NC_000913.3.
WP_001276926.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP30136.
SMRiP30136.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259335. 8 interactors.
DIPiDIP-10982N.
IntActiP30136. 7 interactors.
STRINGi511145.b3994.

Proteomic databases

EPDiP30136.
PaxDbiP30136.
PRIDEiP30136.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76968; AAC76968; b3994.
BAE77325; BAE77325; BAE77325.
GeneIDi948492.
KEGGiecj:JW3958.
eco:b3994.
PATRICi32123511. VBIEscCol129921_4108.

Organism-specific databases

EchoBASEiEB1544.
EcoGeneiEG11585. thiC.

Phylogenomic databases

eggNOGiENOG4105CBF. Bacteria.
COG0422. LUCA.
HOGENOMiHOG000224484.
InParanoidiP30136.
KOiK03147.
OMAiTWELFRD.
PhylomeDBiP30136.

Enzyme and pathway databases

UniPathwayiUPA00060.
BioCyciEcoCyc:THIC-MONOMER.
ECOL316407:JW3958-MONOMER.
MetaCyc:THIC-MONOMER.

Miscellaneous databases

PROiP30136.

Family and domain databases

HAMAPiMF_00089. ThiC. 1 hit.
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...

Entry informationi

Entry nameiTHIC_ECOLI
AccessioniPrimary (citable) accession number: P30136
Secondary accession number(s): Q2M8T1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1993
Last sequence update: October 1, 1993
Last modified: November 2, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.