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Protein

Bifunctional thiamine biosynthesis protein ThiDN

Gene

thiDN

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P.By similarity
Condenses 4-methyl-5-(beta-hydroxyethyl)thiazole monophosphate (THZ-P) and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP).By similarity

Catalytic activityi

ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-2-methyl-5-(phosphomethyl)pyrimidine.By similarity
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine.By similarity
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-((2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene)ethyl phosphate = diphosphate + thiamine phosphate + CO2.By similarity
4-amino-2-methyl-5-diphosphomethylpyrimidine + 2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate = diphosphate + thiamine phosphate + CO2.By similarity
4-amino-2-methyl-5-diphosphomethylpyrimidine + 4-methyl-5-(2-phosphono-oxyethyl)thiazole = diphosphate + thiamine phosphate.By similarity

Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in the subpathway that synthesizes 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole. This subpathway is part of the pathway thiamine diphosphate biosynthesis, which is itself 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.

Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole.
Proteins known to be involved in this subpathway in this organism are:
  1. Bifunctional thiamine biosynthesis protein ThiDN (thiDN)
This subpathway is part of the pathway thiamine diphosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine and 4-methyl-5-(2-phosphoethyl)-thiazole, the pathway thiamine diphosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei41Hydroxymethylpyrimidine/phosphomethylpyrimidineBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Thiamine biosynthesis

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00060; UER00141.

Names & Taxonomyi

Protein namesi
Recommended name:
Bifunctional thiamine biosynthesis protein ThiDN
Including the following 2 domains:
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (EC:2.7.1.49By similarity, EC:2.7.4.7By similarity)
Alternative name(s):
Hydroxymethylpyrimidine kinase
Short name:
HMP kinase
Hydroxymethylpyrimidine phosphate kinase
Short name:
HMP-P kinase
Short name:
HMP-phosphate kinase
Short name:
HMPP kinase
Thiamine-phosphate synthase ThiN (EC:2.5.1.3)
Short name:
TP synthase
Short name:
TPS
Alternative name(s):
Thiamine-phosphate pyrophosphorylase
Short name:
TMP pyrophosphorylase
Short name:
TMP-PPase
Gene namesi
Name:thiDN
Ordered Locus Names:MJ0236
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001067551 – 417Bifunctional thiamine biosynthesis protein ThiDNAdd BLAST417

Interactioni

Protein-protein interaction databases

STRINGi243232.MJ_0236.

Structurei

Secondary structure

1417
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi240 – 255Combined sources16
Beta strandi269 – 272Combined sources4
Helixi279 – 281Combined sources3
Beta strandi282 – 287Combined sources6
Beta strandi289 – 291Combined sources3
Beta strandi295 – 299Combined sources5
Beta strandi303 – 305Combined sources3
Helixi309 – 319Combined sources11
Beta strandi327 – 331Combined sources5
Helixi335 – 341Combined sources7
Turni342 – 344Combined sources3
Beta strandi347 – 349Combined sources3
Helixi352 – 354Combined sources3
Helixi361 – 373Combined sources13
Beta strandi378 – 382Combined sources5
Beta strandi391 – 398Combined sources8
Helixi399 – 414Combined sources16

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PHPX-ray2.03A/B/D/E236-416[»]
ProteinModelPortaliQ57688.
SMRiQ57688.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ57688.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 235Hydroxymethylpyrimidine/phosphomethylpyrimidine kinaseAdd BLAST235
Regioni236 – 417Thiamine-phosphate synthaseAdd BLAST182

Sequence similaritiesi

In the N-terminal section; belongs to the ThiD family.Curated
In the C-terminal section; belongs to the ThiN family.Curated

Phylogenomic databases

eggNOGiarCOG00020. Archaea.
COG0351. LUCA.
COG1992. LUCA.
InParanoidiQ57688.
KOiK00941.

Family and domain databases

CDDicd01169. HMPP_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
3.40.225.10. 1 hit.
InterProiIPR001303. Aldolase_II/adducin_N.
IPR004399. HMP/HMP-P_kinase.
IPR013749. PM/HMP-P_kinase-1.
IPR029056. Ribokinase-like.
IPR019293. ThiN.
[Graphical view]
PfamiPF08543. Phos_pyr_kin. 1 hit.
PF10120. ThiP_synth. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
SSF53639. SSF53639. 1 hit.

Sequencei

Sequence statusi: Complete.

Q57688-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVILAIGGYD PTSGAGISAD IKTAHTLGVY CPTITTSVIP QNNKMVYEKF
60 70 80 90 100
DLPEENIKNQ FKAVFEEFDI EYVKTGVLTK PAIDTLLKYI DKYDLKVICD
110 120 130 140 150
PVLASTTKFS FVDEKLMEKY IELFNKSFLI TPNKEEYKKI MEFIKNNNLM
160 170 180 190 200
IRNDLYILAT GIDDILMKNF KPIKTFKGFR VDKEVHGTGC VYSTAITAFL
210 220 230 240 250
SKGYDLEEAI KEAKRFVLSS VIYAKKSKFG YNSNPTYINK EKVIKNLSYA
260 270 280 290 300
IYLLKKMNFT LIPEVGSNIA ESLPFPKDFK DVAALTGRII KNKLGGFYIV
310 320 330 340 350
GDIEFGASEH IAKIILSASK FNPEIRACMN IKYDGGLIKL LKDKFAVSSF
360 370 380 390 400
DRKEEPPNVS TMEWGTKIAC EKFGGVPDII YDRGGEGKEP MIRVLGRDAI
410
EVVKKVEVIQ KIYNTLM
Length:417
Mass (Da):47,056
Last modified:January 25, 2012 - v2
Checksum:i810246AD46805E27
GO

Sequence cautioni

The sequence AAB98222 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98222.1. Different initiation.
PIRiE64329.
RefSeqiWP_064496432.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98222; AAB98222; MJ_0236.
GeneIDi1451089.
KEGGimja:MJ_0236.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98222.1. Different initiation.
PIRiE64329.
RefSeqiWP_064496432.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PHPX-ray2.03A/B/D/E236-416[»]
ProteinModelPortaliQ57688.
SMRiQ57688.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0236.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98222; AAB98222; MJ_0236.
GeneIDi1451089.
KEGGimja:MJ_0236.

Phylogenomic databases

eggNOGiarCOG00020. Archaea.
COG0351. LUCA.
COG1992. LUCA.
InParanoidiQ57688.
KOiK00941.

Enzyme and pathway databases

UniPathwayiUPA00060; UER00141.

Miscellaneous databases

EvolutionaryTraceiQ57688.

Family and domain databases

CDDicd01169. HMPP_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
3.40.225.10. 1 hit.
InterProiIPR001303. Aldolase_II/adducin_N.
IPR004399. HMP/HMP-P_kinase.
IPR013749. PM/HMP-P_kinase-1.
IPR029056. Ribokinase-like.
IPR019293. ThiN.
[Graphical view]
PfamiPF08543. Phos_pyr_kin. 1 hit.
PF10120. ThiP_synth. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
SSF53639. SSF53639. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiTHIDN_METJA
AccessioniPrimary (citable) accession number: Q57688
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 25, 2012
Last modified: November 30, 2016
This is version 88 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

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.