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P0A5M4 (DCDA_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 65. 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:Rv1293, MT1332
ORF Names:MTCY373.13
OrganismMycobacterium tuberculosis [Reference proteome] [HAMAP]
Taxonomic identifier1773 [NCBI]
Taxonomic lineageBacteria › Actinobacteria › Actinobacteridae › Actinomycetales › Corynebacterineae › Mycobacteriaceae › Mycobacterium › Mycobacterium tuberculosis complex

Protein attributes

Sequence length447 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine Probable. Is essential for the viability of M.tuberculosis in the host. Ref.6

Catalytic activity

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

Cofactor

Pyridoxal phosphate. Ref.6

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; disulfide-linked. Can also form homotetramer at higher protein concentrations. Ref.5 Ref.6 Ref.7

Disruption phenotype

Strains lacking this gene are lysine auxotrophs. They can not survive in immunocompromised mice. Ref.6

Miscellaneous

Was identified as a high-confidence drug target. HAMAP-Rule MF_02120

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 – 447447Diaminopimelate decarboxylase HAMAP-Rule MF_02120
PRO_0000149929

Regions

Region300 – 3034Pyridoxal phosphate binding HAMAP-Rule MF_02120

Sites

Active site3751Proton donor Potential
Binding site2161Substrate
Binding site2581Pyridoxal phosphate; via amide nitrogen
Binding site3031Substrate
Binding site3441Substrate
Binding site3481Substrate
Binding site3761Substrate
Binding site4051Pyridoxal phosphate
Binding site4051Substrate

Amino acid modifications

Modified residue721N6-(pyridoxal phosphate)lysine HAMAP-Rule MF_02120
Disulfide bond93Interchain (with C-375) Ref.6 Ref.7
Disulfide bond375Interchain (with C-72) Ref.6 Ref.7

Experimental info

Sequence conflict3461A → G in AAA25361. Ref.1
Sequence conflict389 – 42638DDIRP…VAVHA → TIFGPAIWLRLPPPALLLFA VESLQHGRPSRCGSGAR in AAA25361. Ref.1

Secondary structure

1 ....................................................................................... 447
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P0A5M4 [UniParc].

Last modified March 15, 2005. Version 1.
Checksum: 3CE085A33F7F30F4

FASTA44747,458
        10         20         30         40         50         60 
MNELLHLAPN VWPRNTTRDE VGVVCIAGIP LTQLAQEYGT PLFVIDEDDF RSRCRETAAA 

        70         80         90        100        110        120 
FGSGANVHYA AKAFLCSEVA RWISEEGLCL DVCTGGELAV ALHASFPPER ITLHGNNKSV 

       130        140        150        160        170        180 
SELTAAVKAG VGHIVVDSMT EIERLDAIAG EAGIVQDVLV RLTVGVEAHT HEFISTAHED 

       190        200        210        220        230        240 
QKFGLSVASG AAMAAVRRVF ATDHLRLVGL HSHIGSQIFD VDGFELAAHR VIGLLRDVVG 

       250        260        270        280        290        300 
EFGPEKTAQI ATVDLGGGLG ISYLPSDDPP PIAELAAKLG TIVSDESTAV GLPTPKLVVE 

       310        320        330        340        350        360 
PGRAIAGPGT ITLYEVGTVK DVDVSATAHR RYVSVDGGMS DNIRTALYGA QYDVRLVSRV 

       370        380        390        400        410        420 
SDAPPVPARL VGKHCESGDI IVRDTWVPDD IRPGDLVAVA ATGAYCYSLS SRYNMVGRPA 

       430        440 
VVAVHAGNAR LVLRRETVDD LLSLEVR

« Hide

References

« Hide 'large scale' references
[1]"Cloning of the lysA gene from Mycobacterium tuberculosis."
Andersen A.B., Hansen E.B.
Gene 124:105-109(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 35801 / TMC 107 / Erdman.
[2]"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence."
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. expand/collapse author list , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G.
Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 25618 / H37Rv.
[3]"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains."
Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. expand/collapse author list , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.
J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CDC 1551 / Oshkosh.
[4]"targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis."
Raman K., Yeturu K., Chandra N.
BMC Syst. Biol. 2:109-109(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
[5]"Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of LysA (Rv1293) from Mycobacterium tuberculosis."
Kefala G., Perry L.J., Weiss M.S.
Acta Crystallogr. F 61:782-784(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION, SUBUNIT.
Strain: ATCC 25618 / H37Rv.
[6]"Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis."
Gokulan K., Rupp B., Pavelka M.S. Jr., Jacobs W.R. Jr., Sacchettini J.C.
J. Biol. Chem. 278:18588-18596(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) IN COMPLEXES WITH PLP AND LYSINE, FUNCTION, COFACTOR, SUBUNIT, DISULFIDE BOND, DISRUPTION PHENOTYPE.
Strain: ATCC 25618 / H37Rv.
[7]"The three-dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation."
Weyand S., Kefala G., Svergun D.I., Weiss M.S.
J. Struct. Funct. Genomics 10:209-217(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.33 ANGSTROMS), SUBUNIT, DISULFIDE BOND.
Strain: ATCC 25618 / H37Rv.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M94109 Genomic DNA. Translation: AAA25361.1.
BX842576 Genomic DNA. Translation: CAA97758.1.
AE000516 Genomic DNA. Translation: AAK45594.1.
AL123456 Genomic DNA. Translation: CCP44050.1.
PIRA70773.
RefSeqNP_215809.1. NC_000962.3.
NP_335780.1. NC_002755.2.
YP_006514669.1. NC_018143.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HKVX-ray2.60A/B1-447[»]
1HKWX-ray2.80A/B1-447[»]
2O0TX-ray2.33A/B/C/D2-447[»]
ProteinModelPortalP0A5M4.
SMRP0A5M4. Positions 2-447.
ModBaseSearch...

Protein-protein interaction databases

STRING83332.Rv1293.

Proteomic databases

PRIDEP0A5M4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAK45594; AAK45594; MT1332.
GeneID13319874.
886960.
924739.
KEGGmtc:MT1332.
mtu:Rv1293.
mtv:RVBD_1293.
PATRIC18124694. VBIMycTub22151_1465.

Organism-specific databases

TubercuListRv1293.

Phylogenomic databases

eggNOGCOG0019.
HOGENOMHOG000045071.
KOK01586.
OMAHPKISTG.
ProtClustDBCLSK791086.

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

EvolutionaryTraceP0A5M4.

Entry information

Entry nameDCDA_MYCTU
AccessionPrimary (citable) accession number: P0A5M4
Secondary accession number(s): L0T7U9, P31848
Entry history
Integrated into UniProtKB/Swiss-Prot: March 15, 2005
Last sequence update: March 15, 2005
Last modified: May 1, 2013
This is version 65 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: 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

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents