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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)
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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei225 – 2251Pyridoxal phosphate; via amide nitrogenUniRule annotation
Binding sitei262 – 2621SubstrateUniRule annotation
Binding sitei298 – 2981SubstrateUniRule annotation
Binding sitei302 – 3021SubstrateUniRule annotation
Active sitei329 – 3291Proton donorSequence analysis
Binding sitei330 – 3301SubstrateUniRule annotation
Binding sitei358 – 3581Pyridoxal phosphateUniRule annotation
Binding sitei358 – 3581SubstrateUniRule annotation

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

BioCyciHPYL85963:GJB9-284-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:jhp_0275
OrganismiHelicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)
Taxonomic identifieri85963 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaEpsilonproteobacteriaCampylobacteralesHelicobacteraceaeHelicobacter
Proteomesi
  • UP000000804 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 405405Diaminopimelate decarboxylasePRO_0000149926Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei46 – 461N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi85963.jhp0275.

Structurei

3D structure databases

ProteinModelPortaliQ9ZME5.
SMRiQ9ZME5. Positions 3-402.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni259 – 2624Pyridoxal 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.
OMAiLKGNKFG.
OrthoDBiEOG6Z9B18.

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.
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.

Q9ZME5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFNYEELFQT YKTPFYLYDF DKIKQAFLNY KEAFKGRKSL ICYALKANSN
60 70 80 90 100
LSILSLLANL GSGADCVSIG EIQRALKAGI KPYKIVFSGV GKSAFEIEQA
110 120 130 140 150
LKLNILFLNV ESFMELKTIE TIAQSLGIKA RISIRINPNI DAKTHPYIST
160 170 180 190 200
GLKENKFGVE EKEALEMFLW AKKSAFLEPV SVHFHIGSQL LDLDPITEAS
210 220 230 240 250
QKVAKIAKSL IALGIDLRFF DVGGGIGVSY ENEETIKLYD YAQGILNSLQ
260 270 280 290 300
GLDLTIICEP GRSIVAESGE LITQVLYEKK AQNKRFVIVD AGMNDFLRPS
310 320 330 340 350
LYHAKHAIRV ITPCGGREIS PCDVVGPVCE SSDTFLKDAN LPELEPGDKL
360 370 380 390 400
AIEKVGAYGS SMASQYNSRP KLLELALEDH KIRVIRKREA LEDLWRLEIE

GLEGV
Length:405
Mass (Da):45,114
Last modified:May 1, 1999 - v1
Checksum:i937BE3DBFFADF038
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001439 Genomic DNA. Translation: AAD05866.1.
PIRiF71950.
RefSeqiWP_000483657.1. NZ_CP011330.1.

Genome annotation databases

EnsemblBacteriaiAAD05866; AAD05866; jhp_0275.
KEGGihpj:jhp_0275.
PATRICi20605193. VBIHelPyl98156_0306.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE001439 Genomic DNA. Translation: AAD05866.1.
PIRiF71950.
RefSeqiWP_000483657.1. NZ_CP011330.1.

3D structure databases

ProteinModelPortaliQ9ZME5.
SMRiQ9ZME5. Positions 3-402.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi85963.jhp0275.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD05866; AAD05866; jhp_0275.
KEGGihpj:jhp_0275.
PATRICi20605193. VBIHelPyl98156_0306.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
KOiK01586.
OMAiLKGNKFG.
OrthoDBiEOG6Z9B18.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciHPYL85963:GJB9-284-MONOMER.

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.
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: J99 / ATCC 700824.

Entry informationi

Entry nameiDCDA_HELPJ
AccessioniPrimary (citable) accession number: Q9ZME5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 1, 1999
Last modified: December 9, 2015
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete 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.