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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript 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 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 sitei257Pyridoxal phosphate; via amide nitrogenUniRule annotation1
Binding sitei302SubstrateUniRule annotation1
Binding sitei343SubstrateUniRule annotation1
Binding sitei347SubstrateUniRule annotation1
Active sitei374Proton donorSequence analysis1
Binding sitei375SubstrateUniRule annotation1
Binding sitei404Pyridoxal phosphateUniRule annotation1
Binding sitei404SubstrateUniRule 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

BioCyciCORYNE:G18NG-10753-MONOMER.
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:Cgl1180, cg1334
OrganismiCorynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
Taxonomic identifieri196627 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesCorynebacteriaceaeCorynebacterium
Proteomesi
  • UP000000582 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001499211 – 445Diaminopimelate decarboxylaseAdd BLAST445

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei75N6-(pyridoxal phosphate)lysineUniRule annotation1

Expressioni

Inductioni

Up-regulated by arginine and repressed by lysine.1 Publication

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi196627.cg1334.

Structurei

3D structure databases

ProteinModelPortaliP09890.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni299 – 302Pyridoxal 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.
KOiK01586.
OMAiTVCEYPL.

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.

P09890-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATVENFNEL PAHVWPRNAV RQEDGVVTVA GVPLPDLAEE YGTPLFVVDE
60 70 80 90 100
DDFRSRCRDM ATAFGGPGNV HYASKAFLTK TIARWVDEEG LALDIASINE
110 120 130 140 150
LGIALAAGFP ASRITAHGNN KGVEFLRALV QNGVGHVVLD SAQELELLDY
160 170 180 190 200
VAAGEGKIQD VLIRVKPGIE AHTHEFIATS HEDQKFGFSL ASGSAFEAAK
210 220 230 240 250
AANNAENLNL VGLHCHVGSQ VFDAEGFKLA AERVLGLYSQ IHSELGVALP
260 270 280 290 300
ELDLGGGYGI AYTAAEEPLN VAEVASDLLT AVGKMAAELG IDAPTVLVEP
310 320 330 340 350
GRAIAGPSTV TIYEVGTTKD VHVDDDKTRR YIAVDGGMSD NIRPALYGSE
360 370 380 390 400
YDARVVSRFA EGDPVSTRIV GSHCESGDIL INDEIYPSDI TSGDFLALAA
410 420 430 440
TGAYCYAMSS RYNAFTRPAV VSVRAGSSRL MLRRETLDDI LSLEA
Length:445
Mass (Da):47,411
Last modified:July 1, 1989 - v1
Checksum:iF7F49A23EAA6CAB3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07563 Genomic DNA. Translation: CAA30445.1.
BA000036 Genomic DNA. Translation: BAB98573.1.
BX927151 Genomic DNA. Translation: CAF19884.1.
X54740 Genomic DNA. Translation: CAA38538.1.
Z21501 Genomic DNA. Translation: CAA79711.1.
PIRiS03827.
RefSeqiNP_600406.1. NC_003450.3.
WP_011014180.1. NC_006958.1.

Genome annotation databases

EnsemblBacteriaiBAB98573; BAB98573; BAB98573.
CAF19884; CAF19884; cg1334.
GeneIDi1019163.
KEGGicgb:cg1334.
cgl:NCgl1133.
PATRICi21494406. VBICorGlu203724_1159.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07563 Genomic DNA. Translation: CAA30445.1.
BA000036 Genomic DNA. Translation: BAB98573.1.
BX927151 Genomic DNA. Translation: CAF19884.1.
X54740 Genomic DNA. Translation: CAA38538.1.
Z21501 Genomic DNA. Translation: CAA79711.1.
PIRiS03827.
RefSeqiNP_600406.1. NC_003450.3.
WP_011014180.1. NC_006958.1.

3D structure databases

ProteinModelPortaliP09890.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi196627.cg1334.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAB98573; BAB98573; BAB98573.
CAF19884; CAF19884; cg1334.
GeneIDi1019163.
KEGGicgb:cg1334.
cgl:NCgl1133.
PATRICi21494406. VBICorGlu203724_1159.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
HOGENOMiHOG000045071.
KOiK01586.
OMAiTVCEYPL.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciCORYNE:G18NG-10753-MONOMER.

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_CORGL
AccessioniPrimary (citable) accession number: P09890
Secondary accession number(s): P41254
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: November 2, 2016
This is version 123 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Both, substrate and product of the catalyzed reaction are critical for cell growth.

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.