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Protein

Diaminopimelate decarboxylase

Gene

lysA

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine (Probable). Is essential for the viability of M.tuberculosis in the host (PubMed:12637582).UniRule annotationCurated1 Publication

Catalytic activityi

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

Cofactori

pyridoxal 5'-phosphate1 Publication

Pathwayi: L-lysine biosynthesis via DAP pathway

This protein is involved in step 1 of the subpathway that synthesizes L-lysine from DL-2,6-diaminopimelate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Diaminopimelate decarboxylase (lysA), Diaminopimelate decarboxylase (lysA)
This subpathway is part of the pathway L-lysine biosynthesis via DAP pathway, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-lysine from DL-2,6-diaminopimelate, the pathway L-lysine biosynthesis via DAP pathway and in Amino-acid biosynthesis.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei216 – 2161Substrate1 Publication
Binding sitei258 – 2581Pyridoxal phosphate; via amide nitrogen1 Publication
Binding sitei303 – 3031Substrate1 Publication
Binding sitei344 – 3441Substrate1 Publication
Binding sitei348 – 3481SubstrateUniRule annotation
Active sitei375 – 3751Proton donorUniRule annotation
Binding sitei376 – 3761Substrate1 Publication
Binding sitei405 – 4051Pyridoxal phosphate1 Publication
Binding sitei405 – 4051Substrate1 Publication

GO - Molecular functioni

  • diaminopimelate decarboxylase activity Source: MTBBASE
  • pyridoxal phosphate binding Source: MTBBASE

GO - Biological processi

  • growth Source: MTBBASE
  • lysine biosynthetic process via diaminopimelate Source: MTBBASE
Complete GO annotation...

Keywords - Molecular functioni

Decarboxylase, Lyase

Keywords - Biological processi

Amino-acid biosynthesis, Lysine biosynthesis

Keywords - Ligandi

Pyridoxal phosphate

Enzyme and pathway databases

BRENDAi4.1.1.20. 3445.
UniPathwayiUPA00034; UER00027.

Names & Taxonomyi

Protein namesi
Recommended name:
Diaminopimelate decarboxylaseUniRule annotation (EC:4.1.1.20UniRule annotation)
Short name:
DAP decarboxylaseUniRule annotation
Short name:
DAPDCUniRule annotation
Gene namesi
Name:lysAUniRule annotation
Ordered Locus Names:Rv1293
ORF Names:MTCY373.13
OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Taxonomic identifieri83332 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
Proteomesi
  • UP000001584 Componenti: Chromosome

Organism-specific databases

TubercuListiRv1293.

Subcellular locationi

GO - Cellular componenti

  • cell wall Source: MTBBASE
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Strains lacking this gene are lysine auxotrophs. They cannot survive in immunocompromised mice.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 447447Diaminopimelate decarboxylasePRO_0000149929Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei72 – 721N6-(pyridoxal phosphate)lysine1 Publication
Disulfide bondi93 – 93Interchain (with C-375)1 Publication
Disulfide bondi375 – 375Interchain (with C-72)1 Publication

Keywords - PTMi

Disulfide bond

Proteomic databases

PaxDbiP9WIU7.

Interactioni

Subunit structurei

Homodimer; disulfide-linked. Can also form homotetramer at higher protein concentrations.3 Publications

Protein-protein interaction databases

STRINGi83332.Rv1293.

Structurei

Secondary structure

1
447
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Turni9 – 113Combined sources
Beta strandi16 – 183Combined sources
Beta strandi20 – 223Combined sources
Beta strandi24 – 263Combined sources
Helixi31 – 388Combined sources
Beta strandi40 – 467Combined sources
Helixi47 – 6014Combined sources
Helixi64 – 663Combined sources
Beta strandi67 – 704Combined sources
Helixi71 – 733Combined sources
Helixi77 – 8610Combined sources
Beta strandi89 – 924Combined sources
Helixi95 – 1039Combined sources
Helixi108 – 1103Combined sources
Beta strandi111 – 1133Combined sources
Helixi120 – 12910Combined sources
Beta strandi132 – 1365Combined sources
Helixi139 – 15214Combined sources
Beta strandi156 – 1638Combined sources
Beta strandi165 – 1706Combined sources
Beta strandi172 – 1787Combined sources
Beta strandi181 – 1866Combined sources
Turni187 – 1904Combined sources
Helixi191 – 20111Combined sources
Beta strandi203 – 2119Combined sources
Beta strandi215 – 2184Combined sources
Helixi222 – 24625Combined sources
Beta strandi252 – 2543Combined sources
Helixi272 – 28918Combined sources
Beta strandi296 – 2994Combined sources
Helixi303 – 3064Combined sources
Beta strandi310 – 32314Combined sources
Beta strandi325 – 3273Combined sources
Beta strandi329 – 3368Combined sources
Turni339 – 3413Combined sources
Helixi344 – 3485Combined sources
Beta strandi354 – 3563Combined sources
Beta strandi365 – 3717Combined sources
Beta strandi373 – 3764Combined sources
Beta strandi380 – 3889Combined sources
Beta strandi396 – 4005Combined sources
Beta strandi403 – 4075Combined sources
Helixi413 – 4153Combined sources
Beta strandi420 – 4256Combined sources
Beta strandi428 – 4336Combined sources
Helixi438 – 4425Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HKVX-ray2.60A/B1-447[»]
1HKWX-ray2.80A/B1-447[»]
2O0TX-ray2.33A/B/C/D2-447[»]
ProteinModelPortaliP9WIU7.
SMRiP9WIU7. Positions 2-447.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni300 – 3034Pyridoxal phosphate bindingUniRule annotation1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
KOiK01586.
OMAiLKGNKFG.
PhylomeDBiP9WIU7.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA. 1 hit.
InterProiIPR009006. 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.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSiPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF50621. SSF50621. 2 hits.
SSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01048. lysA. 1 hit.
PROSITEiPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P9WIU7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNELLHLAPN VWPRNTTRDE VGVVCIAGIP LTQLAQEYGT PLFVIDEDDF
60 70 80 90 100
RSRCRETAAA FGSGANVHYA AKAFLCSEVA RWISEEGLCL DVCTGGELAV
110 120 130 140 150
ALHASFPPER ITLHGNNKSV SELTAAVKAG VGHIVVDSMT EIERLDAIAG
160 170 180 190 200
EAGIVQDVLV RLTVGVEAHT HEFISTAHED QKFGLSVASG AAMAAVRRVF
210 220 230 240 250
ATDHLRLVGL HSHIGSQIFD VDGFELAAHR VIGLLRDVVG EFGPEKTAQI
260 270 280 290 300
ATVDLGGGLG ISYLPSDDPP PIAELAAKLG TIVSDESTAV GLPTPKLVVE
310 320 330 340 350
PGRAIAGPGT ITLYEVGTVK DVDVSATAHR RYVSVDGGMS DNIRTALYGA
360 370 380 390 400
QYDVRLVSRV SDAPPVPARL VGKHCESGDI IVRDTWVPDD IRPGDLVAVA
410 420 430 440
ATGAYCYSLS SRYNMVGRPA VVAVHAGNAR LVLRRETVDD LLSLEVR
Length:447
Mass (Da):47,458
Last modified:April 16, 2014 - v1
Checksum:i3CE085A33F7F30F4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti346 – 3461A → G in AAA25361 (PubMed:8440471).Curated
Sequence conflicti389 – 42638DDIRP…VAVHA → TIFGPAIWLRLPPPALLLFA VESLQHGRPSRCGSGAR in AAA25361 (PubMed:8440471).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M94109 Genomic DNA. Translation: AAA25361.1.
AL123456 Genomic DNA. Translation: CCP44050.1.
PIRiA70773.
RefSeqiNP_215809.1. NC_000962.3.
WP_003406632.1. NZ_KK339370.1.

Genome annotation databases

EnsemblBacteriaiCCP44050; CCP44050; Rv1293.
GeneIDi886960.
KEGGimtu:Rv1293.
mtv:RVBD_1293.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M94109 Genomic DNA. Translation: AAA25361.1.
AL123456 Genomic DNA. Translation: CCP44050.1.
PIRiA70773.
RefSeqiNP_215809.1. NC_000962.3.
WP_003406632.1. NZ_KK339370.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1HKVX-ray2.60A/B1-447[»]
1HKWX-ray2.80A/B1-447[»]
2O0TX-ray2.33A/B/C/D2-447[»]
ProteinModelPortaliP9WIU7.
SMRiP9WIU7. Positions 2-447.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi83332.Rv1293.

Proteomic databases

PaxDbiP9WIU7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCCP44050; CCP44050; Rv1293.
GeneIDi886960.
KEGGimtu:Rv1293.
mtv:RVBD_1293.

Organism-specific databases

TubercuListiRv1293.

Phylogenomic databases

eggNOGiENOG4105CU5. Bacteria.
COG0019. LUCA.
KOiK01586.
OMAiLKGNKFG.
PhylomeDBiP9WIU7.

Enzyme and pathway databases

UniPathwayiUPA00034; UER00027.
BRENDAi4.1.1.20. 3445.

Family and domain databases

Gene3Di2.40.37.10. 1 hit.
3.20.20.10. 1 hit.
HAMAPiMF_02120. LysA. 1 hit.
InterProiIPR009006. 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.
IPR029066. PLP-binding_barrel.
[Graphical view]
PfamiPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSiPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMiSSF50621. SSF50621. 2 hits.
SSF51419. SSF51419. 1 hit.
TIGRFAMsiTIGR01048. lysA. 1 hit.
PROSITEiPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDCDA_MYCTU
AccessioniPrimary (citable) accession number: P9WIU7
Secondary accession number(s): L0T7U9, P0A5M4, P31848
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 16, 2014
Last sequence update: April 16, 2014
Last modified: June 8, 2016
This is version 17 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Was identified as a high-confidence drug target.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
    Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.