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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Aquifex aeolicus (strain VF5)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine.By similarity

Catalytic activityi

Meso-2,6-diaminoheptanedioate = L-lysine + CO2.

Cofactori

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.
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 sitei244 – 2441Pyridoxal phosphate; via amide nitrogenBy similarity
Binding sitei282 – 2821SubstrateBy similarity
Binding sitei318 – 3181SubstrateBy similarity
Binding sitei322 – 3221SubstrateBy similarity
Active sitei348 – 3481Proton donorSequence analysis
Binding sitei349 – 3491SubstrateBy similarity
Binding sitei377 – 3771Pyridoxal phosphateBy similarity
Binding sitei377 – 3771SubstrateBy similarity

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

BioCyciAAEO224324:GJBH-862-MONOMER.
UniPathwayiUPA00034; UER00027.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate decarboxylase (EC:4.1.1.20)
Short name:
DAP decarboxylase
Short name:
DAPDC
Gene namesi
Name:lysA
Ordered Locus Names:aq_1208
OrganismiAquifex aeolicus (strain VF5)
Taxonomic identifieri224324 [NCBI]
Taxonomic lineageiBacteriaAquificaeAquificalesAquificaceaeAquifex
Proteomesi
  • UP000000798 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 420420Diaminopimelate decarboxylasePRO_0000149912Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei65 – 651N6-(pyridoxal phosphate)lysineBy similarity

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi224324.aq_1208.

Structurei

Secondary structure

1
420
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 75Combined sources
Beta strandi11 – 144Combined sources
Beta strandi17 – 204Combined sources
Helixi25 – 328Combined sources
Beta strandi34 – 407Combined sources
Helixi41 – 5414Combined sources
Beta strandi58 – 636Combined sources
Helixi64 – 663Combined sources
Helixi70 – 789Combined sources
Beta strandi82 – 876Combined sources
Helixi88 – 969Combined sources
Helixi101 – 1033Combined sources
Beta strandi104 – 1063Combined sources
Helixi113 – 1219Combined sources
Beta strandi125 – 1295Combined sources
Helixi132 – 14514Combined sources
Beta strandi149 – 1568Combined sources
Helixi180 – 1823Combined sources
Helixi183 – 1919Combined sources
Beta strandi196 – 2027Combined sources
Beta strandi207 – 2115Combined sources
Helixi214 – 23118Combined sources
Beta strandi238 – 2403Combined sources
Helixi258 – 2658Combined sources
Turni266 – 2683Combined sources
Beta strandi274 – 2785Combined sources
Helixi282 – 2854Combined sources
Helixi286 – 2883Combined sources
Beta strandi289 – 30113Combined sources
Beta strandi304 – 3107Combined sources
Turni313 – 3153Combined sources
Helixi318 – 3225Combined sources
Beta strandi328 – 3325Combined sources
Beta strandi340 – 3445Combined sources
Beta strandi346 – 3494Combined sources
Beta strandi353 – 3597Combined sources
Beta strandi368 – 3714Combined sources
Turni375 – 3784Combined sources
Helixi379 – 3813Combined sources
Helixi385 – 3873Combined sources
Beta strandi392 – 3976Combined sources
Beta strandi400 – 4056Combined sources
Helixi410 – 4145Combined sources
Helixi415 – 4173Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2P3EX-ray1.99A/B1-420[»]
ProteinModelPortaliO67262.
SMRiO67262. Positions 2-420.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO67262.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni279 – 2824Pyridoxal phosphate bindingBy similarity

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
HOGENOMiHOG000045070.
InParanoidiO67262.
KOiK01586.
OMAiLKGNKFG.
OrthoDBiPOG091H013X.

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.

O67262-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MELLKEYNPY LEYRDGELFI EGVSLKELAQ TFGTPLYVYS SNFIKERFEA
60 70 80 90 100
YRKAFPDALI CYAVKANFNP HLVKLLGELG AGADIVSGGE LYLAKKAGIP
110 120 130 140 150
PERIVYAGVG KTEKELTDAV DSEILMFNVE SRQELDVLNE IAGKLGKKAR
160 170 180 190 200
IAIRVNPDVD PKTHPYIATG MQKSKFGVDI REAQKEYEYA SKLENLEIVG
210 220 230 240 250
IHCHIGSQIL DISPYREAVE KVVSLYESLT QKGFDIKYLD IGGGLGIKYK
260 270 280 290 300
PEDKEPAPQD LADLLKDLLE NVKAKIILEP GRSIMGNAGI LITQVQFLKD
310 320 330 340 350
KGSKHFIIVD AGMNDLIRPS IYNAYHHIIP VETKERKKVV ADIVGPICET
360 370 380 390 400
GDFLALDREI EEVQRGEYLA VLSAGAYGFA MSSHYNMRPR AAEVLVENGS
410 420
VKLIRKRENY DYIVEPSLDI
Length:420
Mass (Da):46,966
Last modified:August 1, 1998 - v1
Checksum:i4B5E922DBE5338EB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07209.1.
PIRiC70404.
RefSeqiNP_213826.1. NC_000918.1.
WP_010880764.1. NC_000918.1.

Genome annotation databases

EnsemblBacteriaiAAC07209; AAC07209; aq_1208.
GeneIDi1192608.
KEGGiaae:aq_1208.
PATRICi20959642. VBIAquAeo85532_0940.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000657 Genomic DNA. Translation: AAC07209.1.
PIRiC70404.
RefSeqiNP_213826.1. NC_000918.1.
WP_010880764.1. NC_000918.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2P3EX-ray1.99A/B1-420[»]
ProteinModelPortaliO67262.
SMRiO67262. Positions 2-420.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224324.aq_1208.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC07209; AAC07209; aq_1208.
GeneIDi1192608.
KEGGiaae:aq_1208.
PATRICi20959642. VBIAquAeo85532_0940.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
HOGENOMiHOG000045070.
InParanoidiO67262.
KOiK01586.
OMAiLKGNKFG.
OrthoDBiPOG091H013X.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BioCyciAAEO224324:GJBH-862-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO67262.

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_AQUAE
AccessioniPrimary (citable) accession number: O67262
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: August 1, 1998
Last modified: September 7, 2016
This is version 109 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.