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Q58497 (DCDA_METJA) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 92. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·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:MJ1097
OrganismMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) [Reference proteome] [HAMAP]
Taxonomic identifier243232 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus ›

Protein attributes

Sequence length438 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine. Ref.2

Catalytic activity

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

Cofactor

Pyridoxal phosphate. Ref.2

Enzyme regulation

Competitively inhibited by the substrate analog azelaic acid in vitro but not in vivo. Ref.2

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_02120

Subunit structure

Homodimer Probable. Ref.2

Sequence similarities

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

Biophysicochemical properties

Kinetic parameters:

KM=588 µM for meso-2,6-diaminoheptanedioate Ref.2

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 438438Diaminopimelate decarboxylase HAMAP-Rule MF_02120
PRO_0000149941

Regions

Region294 – 2974Pyridoxal phosphate binding HAMAP-Rule MF_02120

Sites

Active site3621Proton donor Potential
Binding site2171Substrate
Binding site2541Pyridoxal phosphate; via amide nitrogen
Binding site2971Substrate
Binding site3331Substrate
Binding site3371Substrate
Binding site3631Substrate
Binding site3911Pyridoxal phosphate
Binding site3911Substrate

Amino acid modifications

Modified residue731N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_02120

Secondary structure

1 ....................................................................................... 438
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q58497 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: DE031EC50FD57326

FASTA43848,900
        10         20         30         40         50         60 
MKIMFLGNDT VEIKDGRFFI DGYDAIELAE KFGTPLYVMS EEQIKINYNR YIEAFKRWEE 

        70         80         90        100        110        120 
ETGKEFIVAY AYKANANLAI TRLLAKLGCG ADVVSGGELY IAKLSNVPSK KIVFNGNCKT 

       130        140        150        160        170        180 
KEEIIMGIEA NIRAFNVDSI SELILINETA KELGETANVA FRINPNVNPK THPKISTGLK 

       190        200        210        220        230        240 
KNKFGLDVES GIAMKAIKMA LEMEYVNVVG VHCHIGSQLT DISPFIEETR KVMDFVVELK 

       250        260        270        280        290        300 
EEGIEIEDVN LGGGLGIPYY KDKQIPTQKD LADAIINTML KYKDKVEMPN LILEPGRSLV 

       310        320        330        340        350        360 
ATAGYLLGKV HHIKETPVTK WVMIDAGMND MMRPAMYEAY HHIINCKVKN EKEVVSIAGG 

       370        380        390        400        410        420 
LCESSDVFGR DRELDKVEVG DVLAIFDVGA YGISMANNYN ARGRPRMVLT SKKGVFLIRE 

       430 
RETYADLIAK DIVPPHLL

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii."
Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G., Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R., Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R., Kirkness E.F., Weinstock K.G. expand/collapse author list , Merrick J.M., Glodek A., Scott J.L., Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R., Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D., Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
Science 273:1058-1073(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440.
[2]"Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor."
Ray S.S., Bonanno J.B., Rajashankar K.R., Pinho M.G., He G., De Lencastre H., Tomasz A., Burley S.K.
Structure 10:1499-1508(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 5-438 IN COMPLEXES WITH PLP; L-LYSINE AND SUBSTRATE ANALOG, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, KINETIC PARAMETERS, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		L77117 Genomic DNA. Translation: AAB99100.1.
PIRH64436.
RefSeqNP_248090.1. NC_000909.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1TUFX-ray2.40A/B5-438[»]
1TWIX-ray2.00A/B/C/D6-438[»]
ProteinModelPortalQ58497.
SMRQ58497. Positions 6-438.
ModBaseSearch...

Protein-protein interaction databases

STRING243232.MJ1097.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAB99100; AAB99100; MJ_1097.
GeneID1451993.
KEGGmja:MJ_1097.

Phylogenomic databases

eggNOGCOG0019.
KOK01586.
OMAHPKISTG.
ProtClustDBCLSK876448.

Enzyme and pathway databases

UniPathwayUPA00034; UER00027.

Family and domain databases

Gene3D2.40.37.10. 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.
[Graphical view]
PfamPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMSSF50621. Racem_decarbox_C. 2 hits.
TIGRFAMsTIGR01048. lysA. 1 hit.
PROSITEPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

DrugBankDB00548. Azelaic Acid.
EvolutionaryTraceQ58497.

Entry information

Entry nameDCDA_METJA
AccessionPrimary (citable) accession number: Q58497
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: May 1, 2013
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Methanococcus jannaschii

Methanococcus jannaschii: entries and gene names

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

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