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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Pyridoxal 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.

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.
OMAiLKGNKFG.
PhylomeDBiP23630.

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.
IPR022657. De-COase2_CS.
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.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]

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.
PATRICi18976493. VBIBacSub10457_2437.

Cross-referencesi

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.

3D structure databases

ProteinModelPortaliP23630.
SMRiP23630.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100012831.

Proteomic databases

PaxDbiP23630.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB14270; CAB14270; BSU23380.
GeneIDi938931.
KEGGibsu:BSU23380.
PATRICi18976493. VBIBacSub10457_2437.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
HOGENOMiHOG000045071.
InParanoidiP23630.
KOiK01586.
OMAiLKGNKFG.
PhylomeDBiP23630.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciBSUB:BSU23380-MONOMER.
MetaCyc:MONOMER-6601.

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.
IPR022657. De-COase2_CS.
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.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDCDA_BACSU
AccessioniPrimary (citable) accession number: P23630
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: April 14, 2009
Last modified: November 2, 2016
This is version 131 of the entry and version 5 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.