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D5VR93 (D5VR93_METIM) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 23. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Diaminopimelate decarboxylase HAMAP-Rule MF_02120
Short name=DAP decarboxylase HAMAP-Rule MF_02120
Short name=DAPDC HAMAP-Rule MF_02120
EC=4.1.1.20 HAMAP-Rule MF_02120
Gene names
Name:lysA HAMAP-Rule MF_02120
Ordered Locus Names:Metin_0426
OrganismMethanocaldococcus infernus (strain DSM 11812 / JCM 15783 / ME) [Complete proteome] [HAMAP]
Taxonomic identifier573063 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Methanococci › Methanococcales › Methanocaldococcaceae › Methanocaldococcus ›

Protein attributes

Sequence length431 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine By similarity. HAMAP-Rule MF_02120

Catalytic activity

Meso-2,6-diaminoheptanedioate = L-lysine + CO2. RuleBase RU003738 HAMAP-Rule MF_02120

Cofactor

Pyridoxal phosphate By similarity. RuleBase RU003738 HAMAP-Rule MF_02120

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. RuleBase RU003738 HAMAP-Rule MF_02120

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_02120

Sequence similarities

Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily. HAMAP-Rule MF_02120

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region287 – 2904Pyridoxal phosphate binding By similarity HAMAP-Rule MF_02120

Sites

Binding site2471Pyridoxal phosphate; via amide nitrogen By similarity HAMAP-Rule MF_02120
Binding site2901Substrate By similarity HAMAP-Rule MF_02120
Binding site3261Substrate By similarity HAMAP-Rule MF_02120
Binding site3301Substrate By similarity HAMAP-Rule MF_02120
Binding site3561Substrate By similarity HAMAP-Rule MF_02120
Binding site3841Pyridoxal phosphate By similarity HAMAP-Rule MF_02120
Binding site3841Substrate By similarity HAMAP-Rule MF_02120

Amino acid modifications

Modified residue681N6-(pyridoxal phosphate)lysine By similarity HAMAP-Rule MF_02120

Sequences

Sequence LengthMass (Da)Tools
D5VR93 [UniParc].

Last modified July 13, 2010. Version 1.
Checksum: 07F2D4C9F03F7288

FASTA43148,476
        10         20         30         40         50         60 
MLGNDTLEIK DRIYIDGYDV IELAERFGTP LYIMSEEQIK INFNRYVEAF KRYEEETGKE 

        70         80         90        100        110        120 
FILAYAYKAN SNLAITKLLA KLGSGADVVS GGELYIAKLS QVPSEKIVFN GNCKIREEII 

       130        140        150        160        170        180 
MGIESEIRAF NVDSISELIM INEIAKELGK EANVAFRINP DVDPKTHPKI STGLKKNKFG 

       190        200        210        220        230        240 
LDTKTALKAI DMALKMENIN FVGLHCHIGS QLTDVSPFVE ATKKMMEFIL KLKEKNIEVR 

       250        260        270        280        290        300 
DLNLGGGLGI PYHKDKEIPT VKDYANSIIE TILKFKDKVE MPNLIIEPGR SIVATAGYLV 

       310        320        330        340        350        360 
GKVWHIKETE VTKWVMIDAG MNDLMRPAMY DAYHHMENAK VKGEKEKVSV AGGLCESSDV 

       370        380        390        400        410        420 
FGRDREIDKV EVGDYIVIFD AGAYGISMSN NYNSRGRPRM ILTSKKGVYI IRERETFSDL 

       430 
IAKDIIPPHL L

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References

[1]"Complete sequence of Methanocaldococcus infernus ME."
US DOE Joint Genome Institute
Lucas S., Copeland A., Lapidus A., Cheng J.-F., Bruce D., Goodwin L., Pitluck S., Munk A.C., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Woyke T.
Submitted (APR-2010) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: DSM 11812 / JCM 15783 / ME.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP002009 Genomic DNA. Translation: ADG13096.1.
RefSeqYP_003616060.1. NC_014122.1.

3D structure databases

ProteinModelPortalD5VR93.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaADG13096; ADG13096; Metin_0426.
GeneID9131430.
KEGGmif:Metin_0426.

Organism-specific databases

CMRSearch...

Phylogenomic databases

HOGENOMHOG000045070.
KOK01586.
OMAHPKISTG.

Enzyme and pathway databases

BioCycMINF573063:GHL3-432-MONOMER.
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.
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. 1 hit.
TIGRFAMsTIGR01048. lysA. 1 hit.
PROSITEPS00878. ODR_DC_2_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameD5VR93_METIM
AccessionPrimary (citable) accession number: D5VR93
Entry history
Integrated into UniProtKB/TrEMBL: July 13, 2010
Last sequence update: July 13, 2010
Last modified: May 1, 2013
This is version 23 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info