Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
Binding sitei244Pyridoxal phosphate; via amide nitrogenBy similarity1
Binding sitei282SubstrateBy similarity1
Binding sitei318SubstrateBy similarity1
Binding sitei322SubstrateBy similarity1
Active sitei348Proton donorSequence analysis1
Binding sitei349SubstrateBy similarity1
Binding sitei377Pyridoxal phosphateBy similarity1
Binding sitei377SubstrateBy similarity1

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

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)DescriptionActionsGraphical viewLength
ChainiPRO_00001499121 – 420Diaminopimelate decarboxylaseAdd BLAST420

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei65N6-(pyridoxal phosphate)lysineBy similarity1

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi224324.aq_1208.

Structurei

Secondary structure

1420
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 7Combined sources5
Beta strandi11 – 14Combined sources4
Beta strandi17 – 20Combined sources4
Helixi25 – 32Combined sources8
Beta strandi34 – 40Combined sources7
Helixi41 – 54Combined sources14
Beta strandi58 – 63Combined sources6
Helixi64 – 66Combined sources3
Helixi70 – 78Combined sources9
Beta strandi82 – 87Combined sources6
Helixi88 – 96Combined sources9
Helixi101 – 103Combined sources3
Beta strandi104 – 106Combined sources3
Helixi113 – 121Combined sources9
Beta strandi125 – 129Combined sources5
Helixi132 – 145Combined sources14
Beta strandi149 – 156Combined sources8
Helixi180 – 182Combined sources3
Helixi183 – 191Combined sources9
Beta strandi196 – 202Combined sources7
Beta strandi207 – 211Combined sources5
Helixi214 – 231Combined sources18
Beta strandi238 – 240Combined sources3
Helixi258 – 265Combined sources8
Turni266 – 268Combined sources3
Beta strandi274 – 278Combined sources5
Helixi282 – 285Combined sources4
Helixi286 – 288Combined sources3
Beta strandi289 – 301Combined sources13
Beta strandi304 – 310Combined sources7
Turni313 – 315Combined sources3
Helixi318 – 322Combined sources5
Beta strandi328 – 332Combined sources5
Beta strandi340 – 344Combined sources5
Beta strandi346 – 349Combined sources4
Beta strandi353 – 359Combined sources7
Beta strandi368 – 371Combined sources4
Turni375 – 378Combined sources4
Helixi379 – 381Combined sources3
Helixi385 – 387Combined sources3
Beta strandi392 – 397Combined sources6
Beta strandi400 – 405Combined sources6
Helixi410 – 414Combined sources5
Helixi415 – 417Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO67262.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni279 – 282Pyridoxal phosphate bindingBy similarity4

Sequence similaritiesi

Phylogenomic databases

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

Family and domain databases

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2P3EX-ray1.99A/B1-420[»]
ProteinModelPortaliO67262.
SMRiO67262.
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.

Miscellaneous databases

EvolutionaryTraceiO67262.

Family and domain databases

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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: November 2, 2016
This is version 111 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.