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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
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 sitei234 – 2341Pyridoxal phosphate; via amide nitrogenUniRule annotation
Binding sitei277 – 2771SubstrateUniRule annotation
Binding sitei312 – 3121SubstrateUniRule annotation
Binding sitei316 – 3161SubstrateUniRule annotation
Active sitei343 – 3431Proton donorSequence analysis
Binding sitei344 – 3441SubstrateUniRule annotation
Binding sitei372 – 3721Pyridoxal phosphateUniRule annotation
Binding sitei372 – 3721SubstrateUniRule 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

BioCyciAFUL224325:GJBC-817-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:AF_0800
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 419419Diaminopimelate decarboxylasePRO_0000149940Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei56 – 561N6-(pyridoxal phosphate)lysineUniRule annotation

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Protein-protein interaction databases

STRINGi224325.AF0800.

Structurei

3D structure databases

ProteinModelPortaliO29458.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni274 – 2774Pyridoxal phosphate bindingUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG02268. Archaea.
COG0019. LUCA.
KOiK01586.
OMAiLKGNKFG.

Family and domain databases

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

O29458-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFSTSDGILT VEGVKVTEIV RETGTPVYVT SRALLERNLE AYKKAFSNEG
60 70 80 90 100
LLYAVKANNN LALMRIIASH GFGADVFSDG ELYLASLAGF RKDMVLFNGN
110 120 130 140 150
SKSRKEIEMG VTAGVKFSVD SLDELRTISK IAKEVGKEVE IAFRVNPDVD
160 170 180 190 200
PKTHPKIATG LRESKFGIPH EMVREAYEMA LKLDGVVPVG IHCHIGSQIL
210 220 230 240 250
DLSPFVHALN KVMDIAVDIE KLGVELSFVD MGGGLGIDYE GKGAPTPKDL
260 270 280 290 300
ASAILPEFEG RKADLTSDPQ LWLEPGRSIV GNTTVLITRV NAVKKGYKNF
310 320 330 340 350
VAVDAGFNVL IRPAMYGSYH RVAVANKMDA EPEEVYTVVG PICESGDVLA
360 370 380 390 400
RDRKLPKVEV GDLIAVFDAG AYGFVMSSQY NGRPRCAEVL VSGDRWDVIR
410
EKESYGDLIE KQRLPEWLL
Length:419
Mass (Da):45,872
Last modified:January 1, 1998 - v1
Checksum:i4EB7CB6BEE932047
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90438.1.
PIRiH69349.
RefSeqiWP_010878303.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB90438; AAB90438; AF_0800.
GeneIDi24794398.
KEGGiafu:AF_0800.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB90438.1.
PIRiH69349.
RefSeqiWP_010878303.1. NC_000917.1.

3D structure databases

ProteinModelPortaliO29458.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0800.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB90438; AAB90438; AF_0800.
GeneIDi24794398.
KEGGiafu:AF_0800.

Phylogenomic databases

eggNOGiarCOG02268. Archaea.
COG0019. LUCA.
KOiK01586.
OMAiLKGNKFG.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciAFUL224325:GJBC-817-MONOMER.

Family and domain databases

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

Entry informationi

Entry nameiDCDA_ARCFU
AccessioniPrimary (citable) accession number: O29458
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: November 11, 2015
This is version 104 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, Reference 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.