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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)DescriptionActionsGraphical viewLength
Binding sitei214Pyridoxal phosphate; via amide nitrogenUniRule annotation1 Publication1
Binding sitei249SubstrateUniRule annotation1
Binding sitei285SubstrateUniRule annotation1
Binding sitei289SubstrateUniRule annotation1
Active sitei314Proton donorUniRule annotation1
Binding sitei315SubstrateUniRule annotation1
Binding sitei343Pyridoxal phosphateUniRule annotation1 Publication1
Binding sitei343SubstrateUniRule annotation1

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001499371 – 386Diaminopimelate decarboxylaseAdd BLAST386

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei46N6-(pyridoxal phosphate)lysineUniRule annotation1

Interactioni

Subunit structurei

Homodimer.UniRule annotation1 Publication

Protein-protein interaction databases

STRINGi243274.TM1517.

Structurei

Secondary structure

1386
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 11Combined sources9
Beta strandi13 – 19Combined sources7
Helixi20 – 33Combined sources14
Turni34 – 36Combined sources3
Beta strandi39 – 44Combined sources6
Helixi45 – 47Combined sources3
Helixi51 – 59Combined sources9
Beta strandi63 – 66Combined sources4
Helixi69 – 77Combined sources9
Helixi82 – 84Combined sources3
Beta strandi85 – 87Combined sources3
Helixi94 – 102Combined sources9
Beta strandi107 – 110Combined sources4
Helixi113 – 122Combined sources10
Beta strandi128 – 134Combined sources7
Turni139 – 141Combined sources3
Helixi143 – 151Combined sources9
Beta strandi152 – 157Combined sources6
Helixi158 – 160Combined sources3
Helixi161 – 168Combined sources8
Beta strandi173 – 177Combined sources5
Beta strandi182 – 184Combined sources3
Helixi188 – 204Combined sources17
Beta strandi207 – 210Combined sources4
Beta strandi219 – 221Combined sources3
Helixi226 – 232Combined sources7
Helixi234 – 237Combined sources4
Beta strandi241 – 247Combined sources7
Helixi249 – 252Combined sources4
Helixi253 – 255Combined sources3
Beta strandi256 – 268Combined sources13
Beta strandi271 – 277Combined sources7
Turni280 – 282Combined sources3
Helixi285 – 288Combined sources4
Beta strandi295 – 297Combined sources3
Beta strandi304 – 310Combined sources7
Beta strandi312 – 315Combined sources4
Beta strandi319 – 327Combined sources9
Beta strandi334 – 339Combined sources6
Beta strandi341 – 344Combined sources4
Helixi345 – 347Combined sources3
Turni351 – 353Combined sources3
Beta strandi358 – 362Combined sources5
Beta strandi368 – 372Combined sources5
Helixi377 – 380Combined sources4
Turni381 – 383Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ9X1K5.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni246 – 249Pyridoxal phosphate bindingUniRule annotation1 Publication4

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

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2YXXX-ray1.70A1-386[»]
ProteinModelPortaliQ9X1K5.
SMRiQ9X1K5.
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.
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

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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: November 2, 2016
This is version 117 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.