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Protein

Phosphomethylpyrimidine synthase

Gene

thiC

Organism
Xanthomonas campestris pv. campestris (strain 8004)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

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.UniRule annotation

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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei230 – 2301SubstrateUniRule annotation
Binding sitei259 – 2591SubstrateUniRule annotation
Binding sitei288 – 2881SubstrateUniRule annotation
Binding sitei324 – 3241SubstrateUniRule annotation
Binding sitei424 – 4241SubstrateUniRule annotation
Metal bindingi428 – 4281ZincUniRule annotation
Binding sitei451 – 4511SubstrateUniRule annotation
Metal bindingi492 – 4921ZincUniRule annotation
Metal bindingi572 – 5721Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi575 – 5751Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation
Metal bindingi580 – 5801Iron-sulfur (4Fe-4S-S-AdoMet)UniRule annotation

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

BioCyciXCAM314565:GCQG-844-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:XC_0846
OrganismiXanthomonas campestris pv. campestris (strain 8004)
Taxonomic identifieri314565 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXanthomonas
Proteomesi
  • UP000000420 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 625625Phosphomethylpyrimidine synthasePRO_0000242318Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi314565.XC_0846.

Structurei

3D structure databases

ProteinModelPortaliQ4UYF2.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni344 – 3463Substrate bindingUniRule annotation
Regioni385 – 3884Substrate bindingUniRule annotation

Sequence similaritiesi

Belongs to the ThiC family.UniRule annotation

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.

Q4UYF2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNAAPTVLLQ QTQTLSAAVT QPIPGSRKIF VQGSRADLQV PMREIVLTRT
60 70 80 90 100
PTLFGGQDNP PLSVYDTSGP YTDPQAAIDL AAGLAPLRAD WIAERGDTLP
110 120 130 140 150
LEALSSSFGR GREHDARLDA VRFPSRRLPR VARSGANVTQ MHYARRGIIT
160 170 180 190 200
PEMEFVAIRE NQRLEAVTDA VLRKQHPGEA FGAAIQQRIT PEFVREEIAR
210 220 230 240 250
GRAILPNNIN HPESEPMIIG RNFLTKINAN IGNSAVSSGI AEEVEKLVWS
260 270 280 290 300
IRWGGDTVMD LSTGKHIHET RDWIIRNSPV PIGTVPIYQA LEKVDGRAEE
310 320 330 340 350
LTWEIFRDTL IEQAEQGVDY FTIHAGVLLR YVPLTARRVT GIVSRGGSIL
360 370 380 390 400
AKWCLAHHKE NFLYTHFEDI CEIMKAYDVA FSLGDGLRPG CIADANDAAQ
410 420 430 440 450
FGELETLGEL TKLAWKHDVQ TMIEGPGHVP MQLIKENMDK QLRECGEAPF
460 470 480 490 500
YTLGPLTTDI APGYDHITSA IGAAMIGWFG TAMLCYVTPK EHLGLPNRQD
510 520 530 540 550
VRDGIMAYKI AAHAADLAKG HPGVQVRDNA LSKARFEFRW DDQFHLGLDP
560 570 580 590 600
EKAKEFHDET LPKDAHKLAH FCSMCGPHFC SMKITQDVRD YAAEHGISED
610 620
HALEAGMQEK SGEFVAQGAQ VYRAS
Length:625
Mass (Da):69,174
Last modified:July 5, 2005 - v1
Checksum:i43EA4014CA3404E8
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000050 Genomic DNA. Translation: AAY47921.1.
RefSeqiWP_011038418.1. NC_007086.1.

Genome annotation databases

EnsemblBacteriaiAAY47921; AAY47921; XC_0846.
KEGGixcb:XC_0846.
PATRICi24063002. VBIXanCam24967_0911.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000050 Genomic DNA. Translation: AAY47921.1.
RefSeqiWP_011038418.1. NC_007086.1.

3D structure databases

ProteinModelPortaliQ4UYF2.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi314565.XC_0846.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAY47921; AAY47921; XC_0846.
KEGGixcb:XC_0846.
PATRICi24063002. VBIXanCam24967_0911.

Phylogenomic databases

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

Enzyme and pathway databases

UniPathwayiUPA00060.
BioCyciXCAM314565:GCQG-844-MONOMER.

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

  1. "Comparative and functional genomic analyses of the pathogenicity of phytopathogen Xanthomonas campestris pv. campestris."
    Qian W., Jia Y., Ren S.-X., He Y.-Q., Feng J.-X., Lu L.-F., Sun Q., Ying G., Tang D.-J., Tang H., Wu W., Hao P., Wang L., Jiang B.-L., Zeng S., Gu W.-Y., Lu G., Rong L.
    , Tian Y., Yao Z., Fu G., Chen B., Fang R., Qiang B., Chen Z., Zhao G.-P., Tang J.-L., He C.
    Genome Res. 15:757-767(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 8004.

Entry informationi

Entry nameiTHIC_XANC8
AccessioniPrimary (citable) accession number: Q4UYF2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: July 5, 2005
Last modified: February 17, 2016
This is version 67 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

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.