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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)
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei227 – 2271Pyridoxal phosphate; via amide nitrogenUniRule annotation
Binding sitei271 – 2711SubstrateUniRule annotation
Binding sitei307 – 3071SubstrateUniRule annotation
Binding sitei311 – 3111SubstrateUniRule annotation
Binding sitei343 – 3431SubstrateUniRule annotation
Binding sitei378 – 3781Pyridoxal phosphateUniRule annotation
Binding sitei378 – 3781SubstrateUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

DecarboxylaseUniRule annotation, Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesisUniRule annotation

Keywords - Ligandi

Pyridoxal 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
OrganismiShigella flexneriImported
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000002673 Componenti: Chromosome
  • UP000001006 Componenti: Chromosome

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei54 – 541N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini32 – 276245Orn_Arg_deC_NInterPro annotationAdd
BLAST
Domaini280 – 395116Orn_DAP_Arg_deCInterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni268 – 2714Pyridoxal phosphate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
KOiK01586.
OMAiSVDMLEQ.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA.
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.

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.
RefSeqiNP_708627.1. NC_004337.2.
WP_001120740.1. NZ_LM651928.1.

Genome annotation databases

EnsemblBacteriaiAAN44334; AAN44334; SF2848.
AAP18160; AAP18160; S3046.
CDX08273; CDX08273; NCTC1_03136.
GeneIDi1025821.
KEGGisfl:SF2848.
sft:NCTC1_03136.
sfx:S3046.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE005674 Genomic DNA. Translation: AAN44334.1.
AE014073 Genomic DNA. Translation: AAP18160.1.
RefSeqiNP_708627.1. NC_004337.2.
WP_001120740.1. NZ_LM651928.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN44334; AAN44334; SF2848.
AAP18160; AAP18160; S3046.
CDX08273; CDX08273; NCTC1_03136.
GeneIDi1025821.
KEGGisfl:SF2848.
sft:NCTC1_03136.
sfx:S3046.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
KOiK01586.
OMAiSVDMLEQ.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA.
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...

Publicationsi

  1. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
    Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
    Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 301Imported and 301 / Serotype 2aImported.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 2457TImported and ATCC 700930 / 2457T / Serotype 2aImported.

Entry informationi

Entry nameiQ83QB7_SHIFL
AccessioniPrimary (citable) accession number: Q83QB7
Secondary accession number(s): Q7C059
Entry historyi
Integrated into UniProtKB/TrEMBL: June 1, 2003
Last sequence update: June 1, 2003
Last modified: July 6, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.