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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Burkholderia phytofirmans (strain DSM 17436 / PsJN)
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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei219 – 2191Pyridoxal phosphate; via amide nitrogenUniRule annotation
Binding sitei263 – 2631SubstrateUniRule annotation
Binding sitei299 – 2991SubstrateUniRule annotation
Binding sitei303 – 3031SubstrateUniRule annotation
Binding sitei334 – 3341SubstrateUniRule annotation
Binding sitei369 – 3691Pyridoxal phosphateUniRule annotation
Binding sitei369 – 3691SubstrateUniRule annotation

GO - Molecular functioni

  1. diaminopimelate decarboxylase activity Source: UniProtKB-HAMAP
  2. pyridoxal phosphate binding Source: UniProtKB-HAMAP

GO - Biological processi

  1. lysine biosynthetic process via diaminopimelate Source: UniProtKB-HAMAP
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

BioCyciBPHY398527:GJEX-7166-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:Bphyt_7089Imported
OrganismiBurkholderia phytofirmans (strain DSM 17436 / PsJN)Imported
Taxonomic identifieri398527 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaeBurkholderia
ProteomesiUP000001739 Componenti: Chromosome 2

PTM / Processingi

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei45 – 451N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi398527.Bphyt_7089.

Structurei

3D structure databases

ProteinModelPortaliB2TA75.
SMRiB2TA75. Positions 6-402.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni260 – 2634Pyridoxal phosphate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0019.
HOGENOMiHOG000045070.
KOiK01586.
OMAiTTKFGIY.
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.
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.

B2TA75-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPFNPQQLVE LAHEHGTPLW VYDADTIRRR IAELRSFDVI RYAQKACSNL
60 70 80 90 100
HILKLMRDEG AMVDAVSLGE IKRSLAAGFK PDGDPEGVVF TADLIDHATL
110 120 130 140 150
ATVIEHRITV NAGSLDMLEQ IGRHAPEGHR VWLRINPGFG HGHSNKTNTG
160 170 180 190 200
GEHSKHGIWL DDVPRAVELV RRYRLKLVGL HMHIGSGVDY GHLSRVCEAM
210 220 230 240 250
VEAVKGLGHD IEAISAGGGL SVPYREGEPD IDVAHYFRLW DAARRQIETH
260 270 280 290 300
VGHRVRLEIE PGRFLVAQSG VLVAEVHALN RRPAQQFALL DAGFNDLVRP
310 320 330 340 350
SFYGSHHEMT VLRRDGALSE APIDSFAVAG PLCEAGDVFT QAESGVITNR
360 370 380 390 400
SIHTPEVGDF IVFHDAGAYG ASMSSNYNSR PLAPEVLLDH GKPRLIRRRQ
410
TIDELLALEE TAA
Length:413
Mass (Da):45,539
Last modified:July 1, 2008 - v1
Checksum:i9F021CE2A1EE4E53
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001053 Genomic DNA. Translation: ACD21377.1.
RefSeqiYP_001890748.1. NC_010676.1.

Genome annotation databases

EnsemblBacteriaiACD21377; ACD21377; Bphyt_7089.
KEGGibpy:Bphyt_7089.
PATRICi19209169. VBIBurPhy117947_3379.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001053 Genomic DNA. Translation: ACD21377.1.
RefSeqiYP_001890748.1. NC_010676.1.

3D structure databases

ProteinModelPortaliB2TA75.
SMRiB2TA75. Positions 6-402.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi398527.Bphyt_7089.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiACD21377; ACD21377; Bphyt_7089.
KEGGibpy:Bphyt_7089.
PATRICi19209169. VBIBurPhy117947_3379.

Phylogenomic databases

eggNOGiCOG0019.
HOGENOMiHOG000045070.
KOiK01586.
OMAiTTKFGIY.
OrthoDBiEOG6Z9B18.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciBPHY398527:GJEX-7166-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.
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. "Complete sequence of chromosome 2 of Burkholderia phytofirmans PsJN."
    Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N.
    , Nowak J., Sessitsch A., Lazarovits G., Compant S., Barka E., Tiedje J.
    Submitted (APR-2008) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 17436 / PsJNImported.

Entry informationi

Entry nameiB2TA75_BURPP
AccessioniPrimary (citable) accession number: B2TA75
Entry historyi
Integrated into UniProtKB/TrEMBL: July 1, 2008
Last sequence update: July 1, 2008
Last modified: April 1, 2015
This is version 50 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

External Data

Dasty 3

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 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.