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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.UniRule annotation

Catalytic activityi

Meso-2,6-diaminoheptanedioate = L-lysine + CO2.UniRule annotation

Cofactori

pyridoxal 5'-phosphateUniRule annotation1 Publication

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes L-lysine from DL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate decarboxylase (lysA), Diaminopimelate decarboxylase (lysA)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-lysine from DL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei214 – 2141Pyridoxal phosphate; via amide nitrogenUniRule annotation1 Publication
Binding sitei249 – 2491SubstrateUniRule annotation
Binding sitei285 – 2851SubstrateUniRule annotation
Binding sitei289 – 2891SubstrateUniRule annotation
Active sitei314 – 3141Proton donorUniRule annotation
Binding sitei315 – 3151SubstrateUniRule annotation
Binding sitei343 – 3431Pyridoxal phosphateUniRule annotation1 Publication
Binding sitei343 – 3431SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate decarboxylaseUniRule annotation (EC:4.1.1.20UniRule annotation)
Short name:
DAP decarboxylaseUniRule annotation
Short name:
DAPDCUniRule annotation
Gene namesi
Name:lysAUniRule annotation
Ordered Locus Names:TM_1517
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 386386Diaminopimelate decarboxylasePRO_0000149937Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei46 – 461N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi243274.TM1517.

Structurei

Secondary structure

1
386
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 119Combined sources
Beta strandi13 – 197Combined sources
Helixi20 – 3314Combined sources
Turni34 – 363Combined sources
Beta strandi39 – 446Combined sources
Helixi45 – 473Combined sources
Helixi51 – 599Combined sources
Beta strandi63 – 664Combined sources
Helixi69 – 779Combined sources
Helixi82 – 843Combined sources
Beta strandi85 – 873Combined sources
Helixi94 – 1029Combined sources
Beta strandi107 – 1104Combined sources
Helixi113 – 12210Combined sources
Beta strandi128 – 1347Combined sources
Turni139 – 1413Combined sources
Helixi143 – 1519Combined sources
Beta strandi152 – 1576Combined sources
Helixi158 – 1603Combined sources
Helixi161 – 1688Combined sources
Beta strandi173 – 1775Combined sources
Beta strandi182 – 1843Combined sources
Helixi188 – 20417Combined sources
Beta strandi207 – 2104Combined sources
Beta strandi219 – 2213Combined sources
Helixi226 – 2327Combined sources
Helixi234 – 2374Combined sources
Beta strandi241 – 2477Combined sources
Helixi249 – 2524Combined sources
Helixi253 – 2553Combined sources
Beta strandi256 – 26813Combined sources
Beta strandi271 – 2777Combined sources
Turni280 – 2823Combined sources
Helixi285 – 2884Combined sources
Beta strandi295 – 2973Combined sources
Beta strandi304 – 3107Combined sources
Beta strandi312 – 3154Combined sources
Beta strandi319 – 3279Combined sources
Beta strandi334 – 3396Combined sources
Beta strandi341 – 3444Combined sources
Helixi345 – 3473Combined sources
Turni351 – 3533Combined sources
Beta strandi358 – 3625Combined sources
Beta strandi368 – 3725Combined sources
Helixi377 – 3804Combined sources
Turni381 – 3833Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YXXX-ray1.70A1-386[»]
ProteinModelPortaliQ9X1K5.
SMRiQ9X1K5. Positions 2-386.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9X1K5.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni246 – 2494Pyridoxal phosphate bindingUniRule annotation1 Publication

Sequence similaritiesi

Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
InParanoidiQ9X1K5.
KOiK01586.
OMAiLKGNKFG.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA. 1 hit.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002986. DAP_deCOOHase_LysA.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR022653. De-COase2_pyr-phos_BS.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSiPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01048. lysA. 1 hit.
PROSITEiPS00878. ODR_DC_2_1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9X1K5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDILRKVAEI HGTPTYVYFE ETLRKRSRLV KEVFEGVNLL PTFAVKANNN
60 70 80 90 100
PVLLKILREE GFGMDVVTKG ELLAAKLAGV PSHTVVWNGN GKSRDQMEHF
110 120 130 140 150
LREDVRIVNV DSFEEMEIWR ELNPEGVEYF IRVNPEVDAK THPHISTGLK
160 170 180 190 200
KHKFGIPLED LDSFMERFRS MNIRGLHVHI GSQITRVEPF VEAFSKVVRA
210 220 230 240 250
SERYGFEEIN IGGGWGINYS GEELDLSSYR EKVVPDLKRF KRVIVEIGRY
260 270 280 290 300
IVAPSGYLLL RVVLVKRRHN KAFVVVDGGM NVLIRPALYS AYHRIFVLGK
310 320 330 340 350
QGKEMRADVV GPLCESGDVI AYDRELPEVE PGDIIAVENA GAYGYTMSNN
360 370 380
YNSTTRPAEV LVRENGRISL IRRRETEMDI FKDVVM
Length:386
Mass (Da):43,982
Last modified:November 1, 1999 - v1
Checksum:iBB6FD6E9E7869CDB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36584.1.
PIRiF72245.
RefSeqiNP_229317.1. NC_000853.1.
WP_004081870.1. NZ_CP011107.1.

Genome annotation databases

EnsemblBacteriaiAAD36584; AAD36584; TM_1517.
GeneIDi897217.
KEGGitma:TM1517.
tmi:THEMA_06715.
tmw:THMA_1549.
PATRICi23937992. VBITheMar51294_1534.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD36584.1.
PIRiF72245.
RefSeqiNP_229317.1. NC_000853.1.
WP_004081870.1. NZ_CP011107.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2YXXX-ray1.70A1-386[»]
ProteinModelPortaliQ9X1K5.
SMRiQ9X1K5. Positions 2-386.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243274.TM1517.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36584; AAD36584; TM_1517.
GeneIDi897217.
KEGGitma:TM1517.
tmi:THEMA_06715.
tmw:THMA_1549.
PATRICi23937992. VBITheMar51294_1534.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
InParanoidiQ9X1K5.
KOiK01586.
OMAiLKGNKFG.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.

Miscellaneous databases

EvolutionaryTraceiQ9X1K5.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA. 1 hit.
InterProiIPR009006. Ala_racemase/Decarboxylase_C.
IPR002986. DAP_deCOOHase_LysA.
IPR022643. De-COase2_C.
IPR022644. De-COase2_N.
IPR022653. De-COase2_pyr-phos_BS.
IPR000183. Orn/DAP/Arg_de-COase.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSiPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01048. lysA. 1 hit.
PROSITEiPS00878. ODR_DC_2_1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDCDA_THEMA
AccessioniPrimary (citable) accession number: Q9X1K5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1999
Last modified: September 7, 2016
This is version 115 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.