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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: -Protein inferred from homologyi

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 annotation

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)
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 sitei248Pyridoxal phosphate; via amide nitrogenUniRule annotation1
Binding sitei293SubstrateUniRule annotation1
Binding sitei330SubstrateUniRule annotation1
Binding sitei334SubstrateUniRule annotation1
Active sitei361Proton donorSequence analysis1
Binding sitei362SubstrateUniRule annotation1
Binding sitei390Pyridoxal phosphateUniRule annotation1
Binding sitei390SubstrateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDecarboxylase, Lyase
Biological processAmino-acid biosynthesis, Lysine biosynthesis
LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyciBSUB:BSU23380-MONOMER
MetaCyc:MONOMER-6601
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
Synonyms:lys
Ordered Locus Names:BSU23380
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001499151 – 439Diaminopimelate decarboxylaseAdd BLAST439

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei66N6-(pyridoxal phosphate)lysineUniRule annotation1

Proteomic databases

PaxDbiP23630
PRIDEiP23630

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012831

Structurei

3D structure databases

ProteinModelPortaliP23630
SMRiP23630
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni290 – 293Pyridoxal phosphate bindingUniRule annotation4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CU5 Bacteria
COG0019 LUCA
HOGENOMiHOG000045071
InParanoidiP23630
KOiK01586
OMAiVVGYICE
PhylomeDBiP23630

Family and domain databases

CDDicd06828 PLPDE_III_DapDC, 1 hit
Gene3Di2.40.37.10, 2 hits
3.20.20.10, 1 hit
HAMAPiMF_02120 LysA, 1 hit
InterProiView protein in InterPro
IPR009006 Ala_racemase/Decarboxylase_C
IPR002986 DAP_deCOOHase_LysA
IPR022643 De-COase2_C
IPR022657 De-COase2_CS
IPR022644 De-COase2_N
IPR022653 De-COase2_pyr-phos_BS
IPR000183 Orn/DAP/Arg_de-COase
IPR029066 PLP-binding_barrel
PANTHERiPTHR43727:SF2 PTHR43727:SF2, 1 hit
PfamiView protein in Pfam
PF02784 Orn_Arg_deC_N, 1 hit
PF00278 Orn_DAP_Arg_deC, 1 hit
PRINTSiPR01181 DAPDCRBXLASE
PR01179 ODADCRBXLASE
SUPFAMiSSF50621 SSF50621, 1 hit
SSF51419 SSF51419, 1 hit
TIGRFAMsiTIGR01048 lysA, 1 hit
PROSITEiView protein in PROSITE
PS00878 ODR_DC_2_1, 1 hit
PS00879 ODR_DC_2_2, 1 hit

Sequencei

Sequence statusi: Complete.

P23630-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFLHGTSRQN QHGHLEIGGV DALYLAEKYG TPLYVYDVAL IRERAKSFKQ
60 70 80 90 100
AFISAGLKAQ VAYASKAFSS VAMIQLAEEE GLSLDVVSGG ELYTAVAAGF
110 120 130 140 150
PAERIHFHGN NKSREELRMA LEHRIGCIVV DNFYEIALLE DLCKETGHSI
160 170 180 190 200
DVLLRITPGV EAHTHDYITT GQEDSKFGFD LHNGQTERAI EQVLQSEHIQ
210 220 230 240 250
LLGVHCHIGS QIFDTAGFVL AAEKIFKKLD EWRDSYSFVS KVLNLGGGFG
260 270 280 290 300
IRYTEDDEPL HATEYVEKII EAVKENASRY GFDIPEIWIE PGRSLVGDAG
310 320 330 340 350
TTLYTVGSQK EVPGVRQYVA VDGGMNDNIR PALYQAKYEA AAANRIGEAH
360 370 380 390 400
DKTVSIAGKC CESGDMLIWD IDLPEVKEGD LLAVFCTGAY GYSMANNYNR
410 420 430
IPRPAVVFVE NGEAHLVVKR ETYEDIVKLD LPFKTGVKQ
Length:439
Mass (Da):48,574
Last modified:April 14, 2009 - v5
Checksum:i5AE8DEACFE43BB30
GO

Sequence cautioni

The sequence BAA12662 differs from that shown. Reason: Erroneous initiation.Curated
The sequence BAA14211 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti90 – 137GELYT…FYEIA → ESYIRLLQQAFRQNASTFME TIRAGKNCGWRLSTASAALW WIISMKSS in BAA14211 (PubMed:1368705).CuratedAdd BLAST48
Sequence conflicti159G → R in BAA14211 (PubMed:1368705).Curated1
Sequence conflicti385 – 388FCTG → LYR in BAA14211 (PubMed:1368705).Curated4

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X17013 Genomic DNA Translation: CAA34876.1 Sequence problems.
L09228 Genomic DNA Translation: AAA67473.1
D90189 Genomic DNA Translation: BAA14211.1 Different initiation.
D84432 Genomic DNA Translation: BAA12662.1 Different initiation.
AL009126 Genomic DNA Translation: CAB14270.1
PIRiS45535 JU0471
RefSeqiNP_390219.1, NC_000964.3
WP_004398851.1, NZ_JNCM01000036.1

Genome annotation databases

EnsemblBacteriaiCAB14270; CAB14270; BSU23380
GeneIDi938931
KEGGibsu:BSU23380
PATRICifig|224308.179.peg.2547

Similar proteinsi

Entry informationi

Entry nameiDCDA_BACSU
AccessioniPrimary (citable) accession number: P23630
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: April 14, 2009
Last modified: May 23, 2018
This is version 138 of the entry and version 5 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome
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Main funding by: National Institutes of Health