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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.
SENT99287:GCTI-647-MONOMER.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 364364Threonine-phosphate decarboxylasePRO_0000163822Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei216 – 2161N6-(pyridoxal phosphate)lysine

Proteomic databases

PaxDbiP97084.
PRIDEiP97084.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

STRINGi99287.STM0644.

Structurei

Secondary structure

1
364
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi7 – 93Combined sources
Helixi13 – 197Combined sources
Helixi23 – 253Combined sources
Beta strandi26 – 283Combined sources
Helixi40 – 489Combined sources
Helixi50 – 545Combined sources
Helixi62 – 7211Combined sources
Helixi76 – 783Combined sources
Beta strandi79 – 846Combined sources
Helixi85 – 9612Combined sources
Beta strandi99 – 1068Combined sources
Helixi110 – 1178Combined sources
Beta strandi121 – 1266Combined sources
Helixi129 – 1313Combined sources
Helixi139 – 1424Combined sources
Beta strandi149 – 1557Combined sources
Turni157 – 1593Combined sources
Helixi165 – 17814Combined sources
Beta strandi181 – 1855Combined sources
Helixi189 – 1913Combined sources
Helixi199 – 2013Combined sources
Beta strandi208 – 2147Combined sources
Turni215 – 2195Combined sources
Turni221 – 2233Combined sources
Beta strandi226 – 2294Combined sources
Helixi233 – 24210Combined sources
Helixi250 – 2589Combined sources
Helixi259 – 2613Combined sources
Helixi263 – 28523Combined sources
Beta strandi290 – 2923Combined sources
Beta strandi296 – 30510Combined sources
Beta strandi306 – 3083Combined sources
Helixi311 – 3166Combined sources
Turni317 – 3193Combined sources
Beta strandi335 – 3395Combined sources
Helixi343 – 35614Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1LC5X-ray1.46A1-364[»]
1LC7X-ray1.80A1-364[»]
1LC8X-ray1.80A1-364[»]
1LKCX-ray1.80A1-364[»]
ProteinModelPortaliP97084.
SMRiP97084. Positions 7-362.
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti6 – 61S → T in AAC79515 (PubMed:9446573).Curated
Sequence conflicti15 – 151A → P in AAC79515 (PubMed:9446573).Curated
Sequence conflicti25 – 251Q → H in AAC79515 (PubMed:9446573).Curated
Sequence conflicti30 – 301S → T in AAC79515 (PubMed:9446573).Curated
Sequence conflicti42 – 454VKRA → LKPP in AAC79515 (PubMed:9446573).Curated

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
EntryMethodResolution (Å)ChainPositionsPDBsum
1LC5X-ray1.46A1-364[»]
1LC7X-ray1.80A1-364[»]
1LC8X-ray1.80A1-364[»]
1LKCX-ray1.80A1-364[»]
ProteinModelPortaliP97084.
SMRiP97084. Positions 7-362.
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.
SENT99287:GCTI-647-MONOMER.
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: September 7, 2016
This is version 110 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.