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A1RPD3 (A1RPD3_SHESW) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 45. 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:Sputw3181_3722
OrganismShewanella sp. (strain W3-18-1) [Complete proteome] [HAMAP] EMBL ABM26528.1
Taxonomic identifier351745 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Alteromonadales › Shewanellaceae › Shewanella

Protein attributes

Sequence length414 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. HAMAP-Rule MF_02120 RuleBase RU003738

Cofactor

Pyridoxal phosphate By similarity. HAMAP-Rule MF_02120 RuleBase RU003738 SAAS SAAS022644

Pathway

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

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

Region273 – 2764Pyridoxal phosphate binding By similarity HAMAP-Rule MF_02120

Sites

Binding site2391Pyridoxal phosphate; via amide nitrogen By similarity HAMAP-Rule MF_02120
Binding site2761Substrate By similarity HAMAP-Rule MF_02120
Binding site3121Substrate By similarity HAMAP-Rule MF_02120
Binding site3161Substrate By similarity HAMAP-Rule MF_02120
Binding site3431Substrate By similarity HAMAP-Rule MF_02120
Binding site3701Pyridoxal phosphate By similarity HAMAP-Rule MF_02120
Binding site3701Substrate By similarity HAMAP-Rule MF_02120

Amino acid modifications

Modified residue601N6-(pyridoxal phosphate)lysine By similarity HAMAP-Rule MF_02120

Sequences

Sequence LengthMass (Da)Tools
A1RPD3 [UniParc].

Last modified February 6, 2007. Version 1.
Checksum: 51114E8664143FBC

FASTA41445,131
        10         20         30         40         50         60 
MDHFLYHNNA LHAEGCQVAD LAKTYGTPLY IYSRATLERH WHAFNNAVMD HPHLICYAVK 

        70         80         90        100        110        120 
ANANLAVLNV LARLGSGFDI VSGGELARVI EAGGSPAKVV FSGVGKTVAE MEQALNLGIY 

       130        140        150        160        170        180 
CFNVESSAEL EQLNLVAGRL GKVAPVSLRI NPDVDAGTHP YISTGLKENK FGIAMDEAEI 

       190        200        210        220        230        240 
VFARAHALPH LKVKGVDCHI GSQLTEIQPF LDAMDRMLAL IDRLAEQGIV IEHFDVGGGL 

       250        260        270        280        290        300 
GVTYDDETPP HPDVYAAALL KRLGNRKLKL IFEPGRAIAA NAGIFVTQVL YLKENSDKRF 

       310        320        330        340        350        360 
AIVDGAMNDL IRPALYSAWQ NIIPVVPRDS EAYEFDIVGP VCETGDFLGK ERKLALAAGD 

       370        380        390        400        410 
LLAVRSSGAY GFAMASNYNT RPRAAEVMVD GEHAFLVRER EKISQLWQGE QLLP

« Hide

References

[1]"Complete sequence of Shewanella sp. W3-18-1."
US DOE Joint Genome Institute
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M. expand/collapse author list , Hauser L., Kyrpides N., Lykidis A., Tiedje J., Richardson P.
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: W3-18-1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000503 Genomic DNA. Translation: ABM26528.1.
RefSeqYP_965082.1. NC_008750.1.

3D structure databases

ProteinModelPortalA1RPD3.
ModBaseSearch...

Protein-protein interaction databases

STRING351745.Sputw3181_3722.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABM26528; ABM26528; Sputw3181_3722.
GeneID4657805.
KEGGshw:Sputw3181_3722.
PATRIC23601378. VBISheSp103602_3898.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0019.
HOGENOMHOG000045070.
KOK01586.
OMAGPICETS.
ProtClustDBCLSK907584.

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. 1 hit.
TIGRFAMsTIGR01048. lysA. 1 hit.
PROSITEPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameA1RPD3_SHESW
AccessionPrimary (citable) accession number: A1RPD3
Entry history
Integrated into UniProtKB/TrEMBL: February 6, 2007
Last sequence update: February 6, 2007
Last modified: May 1, 2013
This is version 45 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