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Protein

Threonine-phosphate decarboxylase

Gene

cobD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Decarboxylates L-threonine-O-3-phosphate to yield (R)-1-amino-2-propanol O-2-phosphate, the precursor for the linkage between the nucleotide loop and the corrin ring in cobalamin.1 Publication

Catalytic activityi

L-threonine O-3-phosphate = (R)-1-aminopropan-2-yl phosphate + CO2.

Cofactori

Pathwayi: adenosylcobalamin biosynthesis

This protein is involved in the pathway adenosylcobalamin biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway adenosylcobalamin biosynthesis and in Cofactor biosynthesis.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Biological processi

Cobalamin biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-12856.
BRENDAi4.1.1.81. 5542.
UniPathwayiUPA00148.

Names & Taxonomyi

Protein namesi
Recommended name:
Threonine-phosphate decarboxylase (EC:4.1.1.81)
Alternative name(s):
L-threonine-O-3-phosphate decarboxylase
Gene namesi
Name:cobD
Ordered Locus Names:STM0644
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001638221 – 364Threonine-phosphate decarboxylaseAdd BLAST364

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei216N6-(pyridoxal phosphate)lysine1

Proteomic databases

PaxDbiP97084.
PRIDEiP97084.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi99287.STM0644.

Structurei

Secondary structure

1364
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi7 – 9Combined sources3
Helixi13 – 19Combined sources7
Helixi23 – 25Combined sources3
Beta strandi26 – 28Combined sources3
Helixi40 – 48Combined sources9
Helixi50 – 54Combined sources5
Helixi62 – 72Combined sources11
Helixi76 – 78Combined sources3
Beta strandi79 – 84Combined sources6
Helixi85 – 96Combined sources12
Beta strandi99 – 106Combined sources8
Helixi110 – 117Combined sources8
Beta strandi121 – 126Combined sources6
Helixi129 – 131Combined sources3
Helixi139 – 142Combined sources4
Beta strandi149 – 155Combined sources7
Turni157 – 159Combined sources3
Helixi165 – 178Combined sources14
Beta strandi181 – 185Combined sources5
Helixi189 – 191Combined sources3
Helixi199 – 201Combined sources3
Beta strandi208 – 214Combined sources7
Turni215 – 219Combined sources5
Turni221 – 223Combined sources3
Beta strandi226 – 229Combined sources4
Helixi233 – 242Combined sources10
Helixi250 – 258Combined sources9
Helixi259 – 261Combined sources3
Helixi263 – 285Combined sources23
Beta strandi290 – 292Combined sources3
Beta strandi296 – 305Combined sources10
Beta strandi306 – 308Combined sources3
Helixi311 – 316Combined sources6
Turni317 – 319Combined sources3
Beta strandi335 – 339Combined sources5
Helixi343 – 356Combined sources14

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LC5X-ray1.46A1-364[»]
1LC7X-ray1.80A1-364[»]
1LC8X-ray1.80A1-364[»]
1LKCX-ray1.80A1-364[»]
ProteinModelPortaliP97084.
SMRiP97084.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP97084.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107QZB. Bacteria.
COG0079. LUCA.
HOGENOMiHOG000288511.
KOiK04720.
OMAiSINPLGM.
PhylomeDBiP97084.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR005860. CobD.
IPR004838. NHTrfase_class1_PyrdxlP-BS.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR01140. L_thr_O3P_dcar. 1 hit.
PROSITEiPS00105. AA_TRANSFER_CLASS_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P97084-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MALFNSAHGG NIREAATVLG ISPDQLLDFS ANINPLGMPV SVKRALIDNL
60 70 80 90 100
DCIERYPDAD YFHLHQALAR HHQVPASWIL AGNGETESIF TVASGLKPRR
110 120 130 140 150
AMIVTPGFAE YGRALAQSGC EIRRWSLREA DGWQLTDAIL EALTPDLDCL
160 170 180 190 200
FLCTPNNPTG LLPERPLLQA IADRCKSLNI NLILDEAFID FIPHETGFIP
210 220 230 240 250
ALKDNPHIWV LRSLTKFYAI PGLRLGYLVN SDDAAMARMR RQQMPWSVNA
260 270 280 290 300
LAALAGEVAL QDSAWQQATW HWLREEGARF YQALCQLPLL TVYPGRANYL
310 320 330 340 350
LLRCEREDID LQRRLLTQRI LIRSCANYPG LDSRYYRVAI RSAAQNERLL
360
AALRNVLTGI APAD
Length:364
Mass (Da):40,766
Last modified:July 19, 2003 - v2
Checksum:iB6613FD0AB6D846C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti6S → T in AAC79515 (PubMed:9446573).Curated1
Sequence conflicti15A → P in AAC79515 (PubMed:9446573).Curated1
Sequence conflicti25Q → H in AAC79515 (PubMed:9446573).Curated1
Sequence conflicti30S → T in AAC79515 (PubMed:9446573).Curated1
Sequence conflicti42 – 45VKRA → LKPP in AAC79515 (PubMed:9446573).Curated4

Mass spectrometryi

Molecular mass is 40666 Da from positions 1 - 364. Determined by ESI. 1 Publication
Molecular mass is 40894 Da from positions 1 - 364. Determined by ESI. With pyridoxal phosphate.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90625 Genomic DNA. Translation: AAC79515.1.
AE006468 Genomic DNA. Translation: AAL19595.1.
RefSeqiNP_459636.1. NC_003197.1.
WP_001173255.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL19595; AAL19595; STM0644.
GeneIDi1252164.
KEGGistm:STM0644.
PATRICi32379641. VBISalEnt20916_0680.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90625 Genomic DNA. Translation: AAC79515.1.
AE006468 Genomic DNA. Translation: AAL19595.1.
RefSeqiNP_459636.1. NC_003197.1.
WP_001173255.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1LC5X-ray1.46A1-364[»]
1LC7X-ray1.80A1-364[»]
1LC8X-ray1.80A1-364[»]
1LKCX-ray1.80A1-364[»]
ProteinModelPortaliP97084.
SMRiP97084.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM0644.

Proteomic databases

PaxDbiP97084.
PRIDEiP97084.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL19595; AAL19595; STM0644.
GeneIDi1252164.
KEGGistm:STM0644.
PATRICi32379641. VBISalEnt20916_0680.

Phylogenomic databases

eggNOGiENOG4107QZB. Bacteria.
COG0079. LUCA.
HOGENOMiHOG000288511.
KOiK04720.
OMAiSINPLGM.
PhylomeDBiP97084.

Enzyme and pathway databases

UniPathwayiUPA00148.
BioCyciMetaCyc:MONOMER-12856.
BRENDAi4.1.1.81. 5542.

Miscellaneous databases

EvolutionaryTraceiP97084.

Family and domain databases

Gene3Di3.40.640.10. 1 hit.
3.90.1150.10. 1 hit.
InterProiIPR004839. Aminotransferase_I/II.
IPR005860. CobD.
IPR004838. NHTrfase_class1_PyrdxlP-BS.
IPR015424. PyrdxlP-dep_Trfase.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
PfamiPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMiSSF53383. SSF53383. 1 hit.
TIGRFAMsiTIGR01140. L_thr_O3P_dcar. 1 hit.
PROSITEiPS00105. AA_TRANSFER_CLASS_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiCOBD_SALTY
AccessioniPrimary (citable) accession number: P97084
Secondary accession number(s): Q8ZQZ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 19, 2003
Last sequence update: July 19, 2003
Last modified: November 2, 2016
This is version 112 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, 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.