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Q9KVL7 (DCDA_VIBCH) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 69. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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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:VC_0125
OrganismVibrio cholerae
Taxonomic identifier666 [NCBI]
Taxonomic lineageBacteria › Proteobacteria › Gammaproteobacteria › Vibrionales › Vibrionaceae › Vibrio

Protein attributes

Sequence length417 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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

Catalytic activity

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

Cofactor

Pyridoxal phosphate By similarity. HAMAP MF_02120

Pathway

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

Subunit structure

Homodimer Probable. Ref.2

Sequence similarities

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 417417Diaminopimelate decarboxylase HAMAP MF_02120
PRO_0000149938

Regions

Region275 – 2784Pyridoxal phosphate binding By similarity

Sites

Active site3441Proton donor Potential
Binding site2401Pyridoxal phosphate; via amide nitrogen By similarity
Binding site2781Substrate By similarity
Binding site3141Substrate By similarity
Binding site3181Substrate By similarity
Binding site3451Substrate By similarity
Binding site3721Pyridoxal phosphate By similarity
Binding site3721Substrate By similarity

Amino acid modifications

Modified residue611N6-(pyridoxal phosphate)lysine By similarity

Secondary structure

1 ........................................................................ 417
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9KVL7 [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: 17BD33D7E4C0836D

FASTA41746,277
        10         20         30         40         50         60 
MDYFNYQEDG QLWAEQVPLA DLANQYGTPL YVYSRATLER HWHAFDKSVG DYPHLICYAV 

        70         80         90        100        110        120 
KANSNLGVLN TLARLGSGFD IVSVGELERV LAAGGDPSKV VFSGVGKTEA EMKRALQLKI 

       130        140        150        160        170        180 
KCFNVESEPE LQRLNKVAGE LGVKAPISLR INPDVDAKTH PYISTGLRDN KFGITFDRAA 

       190        200        210        220        230        240 
QVYRLAHSLP NLDVHGIDCH IGSQLTALAP FIDATDRLLA LIDSLKAEGI HIRHLDVGGG 

       250        260        270        280        290        300 
LGVVYRDELP PQPSEYAKAL LDRLERHRDL ELIFEPGRAI AANAGVLVTK VEFLKHTEHK 

       310        320        330        340        350        360 
NFAIIDAAMN DLIRPALYQA WQDIIPLRPR QGEAQTYDLV GPVCETSDFL GKDRDLVLQE 

       370        380        390        400        410 
GDLLAVRSSG AYGFTMSSNY NTRPRVAEVM VDGNKTYLVR QREELSSLWA LESVLPE

« Hide

References

« Hide 'large scale' references
[1]"DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae."
Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L., Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R., Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D., Vamathevan J.J., Bass S. expand/collapse author list , Qin H., Dragoi I., Sellers P., McDonald L.A., Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L., Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.
Nature 406:477-483(2000) [PubMed: 10952301] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 39315 / El Tor Inaba N16961 / Serotype O1.
[2]"1.8 Angstrom resolution crystal structure of diaminopimelate decarboxylase (lysA) from Vibrio cholerae."
Center for Structural Genomics of Infectious Diseases (CSGID)
Submitted (JUN-2010) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS), SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE003852 Genomic DNA. Translation: AAF93302.1.
PIRF82360.
RefSeqNP_229783.1. NC_002505.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3N2BX-ray1.80A/B/C/D1-417[»]
ProteinModelPortalQ9KVL7.
ModBaseSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID2615366.
GenomeReviewsGene locus VC_0125 in contig AE003852_GR.
KEGGvch:VC0125.
PATRIC20079294. VBIVibCho83274_0116.
TIGRVC_0125.

Phylogenomic databases

HOGENOMHBG672375.
OMADAHTHPY.
PhylomeDBQ9KVL7.
ProtClustDBCLSK873868.

Family and domain databases

HAMAPMF_02120. LysA.
[Tree]
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]
Gene3DG3DSA:2.40.37.10. Ala_racemase/Decarboxylase_C. 1 hit.
KOK01586.
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 nameDCDA_VIBCH
AccessionPrimary (citable) accession number: Q9KVL7
Entry history
Integrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: October 1, 2000
Last modified: January 25, 2012
This is version 69 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

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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