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P00861 (DCDA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 133. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate decarboxylase

Short name=DAP decarboxylase
Short name=DAPDC
EC=4.1.1.20
Gene names
Name:lysA
Ordered Locus Names:b2838, JW2806
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length420 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. Is not active against the DD- or LL-isomers of diaminopimelate. Ref.4 Ref.8 Ref.9

Catalytic activity

Meso-2,6-diaminoheptanedioate = L-lysine + CO2. Ref.4 Ref.8 Ref.9

Cofactor

Pyridoxal phosphate. Ref.4 Ref.8

Enzyme regulation

Is activated by 2,3-dimercaptopropan-1-ol. Ref.4

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. Ref.4

Induction

Up-regulated by LysR. Repressed in the presence of lysine. Ref.4 Ref.5 Ref.6

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

KM=1.7 mM for meso-2,6-diaminoheptanedioate (at pH 6.8 and 37 degrees Celsius) (Ref.4) Ref.4 Ref.9

KM=1.07 mM for meso-2,6-diaminoheptanedioate (at pH 8) (Ref.4)

pH dependence:

Optimum pH is 6.7-6.8.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

cpxRP0AE882EBI-553837,EBI-550918

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 420420Diaminopimelate decarboxylase HAMAP-Rule MF_02120
PRO_0000149923

Regions

Region268 – 2714Pyridoxal phosphate binding HAMAP-Rule MF_02120

Sites

Active site3421Proton donor Potential
Binding site1911Substrate
Binding site2271Pyridoxal phosphate; via amide nitrogen
Binding site2711Substrate
Binding site3071Substrate
Binding site3111Substrate
Binding site3431Substrate
Binding site3781Pyridoxal phosphate
Binding site3781Substrate
Binding site3821Substrate

Amino acid modifications

Modified residue541N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_02120

Secondary structure

.................................................................................. 420
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00861 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 0A26ABCFAF8462B5

FASTA42046,177
        10         20         30         40         50         60 
MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR FAQKACSNIH 

        70         80         90        100        110        120 
ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT ADVIDQATLE RVSELQIPVN 

       130        140        150        160        170        180 
AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG HSQKTNTGGE NSKHGIWYTD LPAALDVIQR 

       190        200        210        220        230        240 
HHLQLVGIHM HIGSGVDYAH LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD 

       250        260        270        280        290        300 
TEHYYGLWNA AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA 

       310        320        330        340        350        360 
GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ QEGGNVETRA 

       370        380        390        400        410        420 
LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG QARLIRRRQT IEELLALELL 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J01614 Genomic DNA. Translation: AAA83861.1.
U29581 Genomic DNA. Translation: AAB40485.1.
U00096 Genomic DNA. Translation: AAC75877.1.
AP009048 Genomic DNA. Translation: BAE76907.1.
PIRDCECD. A01078.
RefSeqNP_417315.1. NC_000913.3.
YP_491043.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1KNWX-ray2.10A1-420[»]
1KO0X-ray2.20A1-420[»]
ProteinModelPortalP00861.
SMRP00861. Positions 2-411.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10132N.
IntActP00861. 9 interactions.
MINTMINT-1292495.
STRING511145.b2838.

2D gel databases

SWISS-2DPAGEP00861.

Proteomic databases

PaxDbP00861.
PRIDEP00861.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75877; AAC75877; b2838.
BAE76907; BAE76907; BAE76907.
GeneID12932897.
947313.
KEGGecj:Y75_p2772.
eco:b2838.
PATRIC32121094. VBIEscCol129921_2936.

Organism-specific databases

EchoBASEEB0544.
EcoGeneEG10549. lysA.

Phylogenomic databases

eggNOGCOG0019.
HOGENOMHOG000045070.
KOK01586.
OMAVFTQQAG.
OrthoDBEOG6Z9B18.
PhylomeDBP00861.

Enzyme and pathway databases

BioCycEcoCyc:DIAMINOPIMDECARB-MONOMER.
ECOL316407:JW2806-MONOMER.
MetaCyc:DIAMINOPIMDECARB-MONOMER.
UniPathwayUPA00034; UER00027.

Gene expression databases

GenevestigatorP00861.

Family and domain databases

Gene3D2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPMF_02120. LysA.
InterProIPR009006. 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]
PfamPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMSSF50621. SSF50621. 1 hit.
SSF51419. SSF51419. 1 hit.
TIGRFAMsTIGR01048. lysA. 1 hit.
PROSITEPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00861.
PROP00861.

Entry information

Entry nameDCDA_ECOLI
AccessionPrimary (citable) accession number: P00861
Secondary accession number(s): Q2M9Z9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: June 11, 2014
This is version 133 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene