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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: -Experimental evidence at protein leveli

Functioni

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

Miscellaneous

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

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

Keywordsi

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

Secondary structure

1445
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 7Combined sources4
Turni12 – 14Combined sources3
Beta strandi19 – 21Combined sources3
Beta strandi25 – 29Combined sources5
Helixi34 – 41Combined sources8
Beta strandi43 – 49Combined sources7
Helixi50 – 63Combined sources14
Helixi67 – 69Combined sources3
Beta strandi70 – 73Combined sources4
Helixi74 – 76Combined sources3
Helixi80 – 88Combined sources9
Beta strandi92 – 95Combined sources4
Helixi98 – 106Combined sources9
Helixi111 – 113Combined sources3
Beta strandi114 – 116Combined sources3
Helixi123 – 132Combined sources10
Beta strandi135 – 139Combined sources5
Helixi142 – 155Combined sources14
Beta strandi159 – 166Combined sources8
Beta strandi168 – 171Combined sources4
Beta strandi176 – 178Combined sources3
Beta strandi184 – 190Combined sources7
Helixi194 – 204Combined sources11
Beta strandi208 – 214Combined sources7
Beta strandi218 – 221Combined sources4
Helixi225 – 245Combined sources21
Beta strandi251 – 253Combined sources3
Helixi271 – 289Combined sources19
Beta strandi295 – 298Combined sources4
Helixi302 – 305Combined sources4
Beta strandi309 – 326Combined sources18
Beta strandi328 – 335Combined sources8
Turni338 – 340Combined sources3
Helixi343 – 347Combined sources5
Beta strandi353 – 358Combined sources6
Beta strandi364 – 370Combined sources7
Beta strandi372 – 375Combined sources4
Beta strandi379 – 387Combined sources9
Beta strandi395 – 399Combined sources5
Turni402 – 405Combined sources4
Helixi406 – 408Combined sources3
Helixi412 – 414Combined sources3
Beta strandi419 – 424Combined sources6
Beta strandi427 – 432Combined sources6
Helixi437 – 442Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5X7MX-ray2.40A/B1-445[»]
5X7NX-ray1.72A/B1-445[»]
ProteinModelPortaliP09890
SMRiP09890
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
OMAiVVGYICE

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.

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
PATRICifig|196627.13.peg.1159

Similar proteinsi

Entry informationi

Entry nameiDCDA_CORGL
AccessioniPrimary (citable) accession number: P09890
Secondary accession number(s): P41254
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: July 1, 1989
Last modified: March 28, 2018
This is version 130 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome
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Main funding by: National Institutes of Health