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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Shigella flexneri
Status
Unreviewed-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 annotationSAAS 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), 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 sitei227Pyridoxal phosphate; via amide nitrogenUniRule annotation1
Binding sitei271SubstrateUniRule annotation1
Binding sitei307SubstrateUniRule annotation1
Binding sitei311SubstrateUniRule annotation1
Binding sitei343SubstrateUniRule annotation1
Binding sitei378Pyridoxal phosphateUniRule annotation1
Binding sitei378SubstrateUniRule annotation1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDecarboxylaseUniRule annotation, Lyase
Biological processAmino-acid biosynthesis, Lysine biosynthesisUniRule annotation
LigandPyridoxal phosphateUniRule annotationSAAS annotation

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 annotationImported
Ordered Locus Names:S3046Imported, SF2848Imported
ORF Names:CBL25_08445Imported
OrganismiShigella flexneriImported
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeShigella
Proteomesi
  • UP000002673 Componenti: Chromosome
  • UP000195900 Componenti: Unassembled WGS sequence
  • UP000001006 Componenti: Chromosome

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei54N6-(pyridoxal phosphate)lysineUniRule annotation1

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 376Orn_DAP_Arg_deCInterPro annotationAdd BLAST348
Domaini33 – 275Orn_Arg_deC_NInterPro annotationAdd BLAST243

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni268 – 271Pyridoxal 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.
KOiK01586.
OMAiVVGYICE.

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.
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.

Q83QB7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFEVVR
60 70 80 90 100
FAQKACSNIH ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT
110 120 130 140 150
ADVIDQATLE RVSELQIPVN AGSVDTLDQL GQVSPGHRVW LRVNPGFGHG
160 170 180 190 200
HSQKTNTGGE NSKHGIWYTD LPAALDVIQR HHLQLVGIHM HIGSGVDYAH
210 220 230 240 250
LEQVCGAMVR QVIEFGQDLQ AISAGGGLSI PYQQGEEAVD TEHYYGLWNA
260 270 280 290 300
AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
310 320 330 340 350
GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ
360 370 380 390 400
QEGGNVETRA LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG
410 420
QARLIRRRQT IEELLALELL
Length:420
Mass (Da):46,175
Last modified:June 1, 2003 - v1
Checksum:i5CF953BC40B338F9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN44334.1.
AE014073 Genomic DNA. Translation: AAP18160.1.
NGWD01000028 Genomic DNA. Translation: OUZ76589.1.
RefSeqiNP_708627.1. NC_004337.2.
WP_001120740.1. NZ_NMXZ01000028.1.

Genome annotation databases

EnsemblBacteriaiAAN44334; AAN44334; SF2848.
AAP18160; AAP18160; S3046.
GeneIDi1025821.
KEGGisfl:SF2848.
sft:NCTC1_03136.
sfx:S3046.
PATRICifig|198214.7.peg.3389.

Similar proteinsi

Entry informationi

Entry nameiQ83QB7_SHIFL
AccessioniPrimary (citable) accession number: Q83QB7
Secondary accession number(s): Q7C059
Entry historyiIntegrated into UniProtKB/TrEMBL: June 1, 2003
Last sequence update: June 1, 2003
Last modified: November 22, 2017
This is version 121 of the entry and version 1 of the sequence. See complete history.
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported