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P00861

- DCDA_ECOLI

UniProt

P00861 - DCDA_ECOLI

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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. Is not active against the DD- or LL-isomers of diaminopimelate.3 Publications

Catalytic activityi

Meso-2,6-diaminoheptanedioate = L-lysine + CO2.3 Publications

Cofactori

Pyridoxal phosphate.2 Publications

Enzyme regulationi

Is activated by 2,3-dimercaptopropan-1-ol.1 Publication

Kineticsi

  1. KM=1.7 mM for meso-2,6-diaminoheptanedioate (at pH 6.8 and 37 degrees Celsius)2 Publications
  2. KM=1.07 mM for meso-2,6-diaminoheptanedioate (at pH 8)2 Publications

pH dependencei

Optimum pH is 6.7-6.8.1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei191 – 1911Substrate
Binding sitei227 – 2271Pyridoxal phosphate; via amide nitrogen
Binding sitei271 – 2711Substrate
Binding sitei307 – 3071Substrate
Binding sitei311 – 3111Substrate
Active sitei342 – 3421Proton donorSequence Analysis
Binding sitei343 – 3431Substrate
Binding sitei378 – 3781Pyridoxal phosphate
Binding sitei378 – 3781Substrate
Binding sitei382 – 3821Substrate

GO - Molecular functioni

  1. diaminopimelate decarboxylase activity Source: EcoCyc
  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

Decarboxylase, Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:DIAMINOPIMDECARB-MONOMER.
ECOL316407:JW2806-MONOMER.
MetaCyc:DIAMINOPIMDECARB-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:b2838, JW2806
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

Organism-specific databases

EcoGeneiEG10549. lysA.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 420420Diaminopimelate decarboxylasePRO_0000149923Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei54 – 541N6-(pyridoxal phosphate)lysine

Proteomic databases

PaxDbiP00861.
PRIDEiP00861.

2D gel databases

SWISS-2DPAGEP00861.

Expressioni

Inductioni

Up-regulated by LysR. Repressed in the presence of lysine.2 Publications

Gene expression databases

GenevestigatoriP00861.

Interactioni

Binary interactionsi

WithEntry#Exp.IntActNotes
cpxRP0AE882EBI-553837,EBI-550918

Protein-protein interaction databases

DIPiDIP-10132N.
IntActiP00861. 9 interactions.
MINTiMINT-1292495.
STRINGi511145.b2838.

Structurei

Secondary structure

1
420
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni5 – 73
Beta strandi9 – 113
Helixi14 – 2411
Beta strandi26 – 327
Helixi33 – 419
Turni42 – 454
Beta strandi46 – 527
Helixi53 – 553
Helixi59 – 679
Beta strandi71 – 744
Helixi77 – 859
Turni90 – 923
Beta strandi96 – 1027
Helixi106 – 11510
Beta strandi119 – 1235
Helixi124 – 13310
Beta strandi138 – 1447
Beta strandi152 – 1554
Beta strandi157 – 1593
Beta strandi165 – 1673
Helixi168 – 1703
Helixi171 – 18010
Beta strandi184 – 1896
Helixi198 – 21518
Beta strandi220 – 2234
Helixi241 – 25919
Beta strandi264 – 2674
Helixi271 – 2744
Helixi275 – 2773
Beta strandi278 – 29013
Beta strandi293 – 2997
Turni302 – 3043
Helixi307 – 3115
Beta strandi317 – 3204
Beta strandi332 – 3387
Beta strandi340 – 3434
Beta strandi347 – 3504
Beta strandi359 – 3624
Beta strandi369 – 3724
Beta strandi376 – 3794
Helixi380 – 3823
Turni386 – 3883
Beta strandi394 – 3985
Beta strandi401 – 4066
Helixi411 – 4155
Turni416 – 4183

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KNWX-ray2.10A1-420[»]
1KO0X-ray2.20A1-420[»]
ProteinModelPortaliP00861.
SMRiP00861. Positions 2-411.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00861.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni268 – 2714Pyridoxal phosphate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0019.
HOGENOMiHOG000045070.
InParanoidiP00861.
KOiK01586.
OMAiVFTQQAG.
OrthoDBiEOG6Z9B18.
PhylomeDBiP00861.

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.

P00861-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR
60 70 80 90 100
FAQKACSNIH ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT
110 120 130 140 150
ADVIDQATLE RVSELQIPVN AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG
160 170 180 190 200
HSQKTNTGGE NSKHGIWYTD LPAALDVIQR HHLQLVGIHM HIGSGVDYAH
210 220 230 240 250
LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD TEHYYGLWNA
260 270 280 290 300
AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA
310 320 330 340 350
GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ
360 370 380 390 400
QEGGNVETRA LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG
410 420
QARLIRRRQT IEELLALELL
Length:420
Mass (Da):46,177
Last modified:July 21, 1986 - v1
Checksum:i0A26ABCFAF8462B5
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01614 Genomic DNA. Translation: AAA83861.1.
U29581 Genomic DNA. Translation: AAB40485.1.
U00096 Genomic DNA. Translation: AAC75877.1.
AP009048 Genomic DNA. Translation: BAE76907.1.
PIRiA01078. DCECD.
RefSeqiNP_417315.1. NC_000913.3.
YP_491043.1. NC_007779.1.

Genome annotation databases

EnsemblBacteriaiAAC75877; AAC75877; b2838.
BAE76907; BAE76907; BAE76907.
GeneIDi12932897.
947313.
KEGGiecj:Y75_p2772.
eco:b2838.
PATRICi32121094. VBIEscCol129921_2936.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
J01614 Genomic DNA. Translation: AAA83861.1 .
U29581 Genomic DNA. Translation: AAB40485.1 .
U00096 Genomic DNA. Translation: AAC75877.1 .
AP009048 Genomic DNA. Translation: BAE76907.1 .
PIRi A01078. DCECD.
RefSeqi NP_417315.1. NC_000913.3.
YP_491043.1. NC_007779.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1KNW X-ray 2.10 A 1-420 [» ]
1KO0 X-ray 2.20 A 1-420 [» ]
ProteinModelPortali P00861.
SMRi P00861. Positions 2-411.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-10132N.
IntActi P00861. 9 interactions.
MINTi MINT-1292495.
STRINGi 511145.b2838.

2D gel databases

SWISS-2DPAGE P00861.

Proteomic databases

PaxDbi P00861.
PRIDEi P00861.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAC75877 ; AAC75877 ; b2838 .
BAE76907 ; BAE76907 ; BAE76907 .
GeneIDi 12932897.
947313.
KEGGi ecj:Y75_p2772.
eco:b2838.
PATRICi 32121094. VBIEscCol129921_2936.

Organism-specific databases

EchoBASEi EB0544.
EcoGenei EG10549. lysA.

Phylogenomic databases

eggNOGi COG0019.
HOGENOMi HOG000045070.
InParanoidi P00861.
KOi K01586.
OMAi VFTQQAG.
OrthoDBi EOG6Z9B18.
PhylomeDBi P00861.

Enzyme and pathway databases

UniPathwayi UPA00034 ; UER00027 .
BioCyci EcoCyc:DIAMINOPIMDECARB-MONOMER.
ECOL316407:JW2806-MONOMER.
MetaCyc:DIAMINOPIMDECARB-MONOMER.

Miscellaneous databases

EvolutionaryTracei P00861.
PROi P00861.

Gene expression databases

Genevestigatori P00861.

Family and domain databases

Gene3Di 2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPi MF_02120. LysA.
InterProi IPR009006. 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 ]
Pfami PF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view ]
PRINTSi PR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMi SSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsi TIGR01048. lysA. 1 hit.
PROSITEi PS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. II. Nucleotide sequence of the lysA gene and its regulatory region."
    Stragier P., Danos O., Patte J.-C.
    J. Mol. Biol. 168:321-331(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Purification and properties of diaminopimelate decarboxylase from Escherichia coli."
    White P.J., Kelly B.
    Biochem. J. 96:75-84(1965) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY.
    Strain: ATCC 9637 / CCM 2024 / DSM 1116 / NCIMB 8666 / NRRL B-766 / W.
  5. "Regulatory pattern of the Escherichia coli lysA gene: expression of chromosomal lysA-lacZ fusions."
    Stragier P., Borne F., Richaud F., Richaud C., Patte J.C.
    J. Bacteriol. 156:1198-1203(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  6. "Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. I. Identification of a lysR gene encoding an activator of the lysA gene."
    Stragier P., Richaud F., Borne F., Patte J.C.
    J. Mol. Biol. 168:307-320(1983) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  7. "Escherichia coli proteome analysis using the gene-protein database."
    VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
    Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY 2D-GEL.
  8. "Crystallization of diaminopimelate decarboxylase from Escherichia coli, a stereospecific D-amino-acid decarboxylase."
    Momany C., Levdikov V., Blagova L., Crews K.
    Acta Crystallogr. D 58:549-552(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: CRYSTALLIZATION, FUNCTION, CATALYTIC ACTIVITY, COFACTOR.
  9. "The catalytic intermediate stabilized by a 'down' active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis."
    Hu T., Wu D., Chen J., Ding J., Jiang H., Shen X.
    J. Biol. Chem. 283:21284-21293(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS.
    Strain: K12 / JM109 / ATCC 53323.
  10. "Diaminopimelate decarboxylase uses a versatile active site for stereospecific decarboxylation."
    Levdikov V., Blagova L., Bose N., Momany C.
    Submitted (FEB-2009) to the PDB data bank
    Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEXES WITH PYRIDOXAL PHOSPHATE AND LYSINE.

Entry informationi

Entry nameiDCDA_ECOLI
AccessioniPrimary (citable) accession number: P00861
Secondary accession number(s): Q2M9Z9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: October 29, 2014
This is version 135 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. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3