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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)DescriptionActionsGraphical viewLength
Binding sitei219Substrate1
Binding sitei248Substrate1
Binding sitei277Substrate1
Binding sitei313Substrate1
Binding sitei413Substrate1
Metal bindingi417Zinc1
Binding sitei440Substrate1
Metal bindingi481Zinc1
Metal bindingi561Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi564Iron-sulfur (4Fe-4S-S-AdoMet)1
Metal bindingi569Iron-sulfur (4Fe-4S-S-AdoMet)1

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)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 binding3
Regioni374 – 377Substrate binding4

Sequence similaritiesi

Belongs to the ThiC family.Curated

Phylogenomic databases

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

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.

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
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...

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.

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. 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_CAUCR
AccessioniPrimary (citable) accession number: Q9A6Q5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: June 1, 2001
Last modified: November 2, 2016
This is version 87 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.