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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)DescriptionActionsGraphical viewLength
Binding sitei216Substrate1 Publication1
Binding sitei258Pyridoxal phosphate; via amide nitrogen1 Publication1
Binding sitei303Substrate1 Publication1
Binding sitei344Substrate1 Publication1
Binding sitei348SubstrateUniRule annotation1
Active sitei375Proton donorUniRule annotation1
Binding sitei376Substrate1 Publication1
Binding sitei405Pyridoxal phosphate1 Publication1
Binding sitei405Substrate1 Publication1

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

BioCyciMTBH37RV:G185E-5467-MONOMER.
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)DescriptionActionsGraphical viewLength
ChainiPRO_00001499291 – 447Diaminopimelate decarboxylaseAdd BLAST447

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei72N6-(pyridoxal phosphate)lysine1 Publication1
Disulfide bondi93Interchain (with C-375)1 Publication
Disulfide bondi375Interchain (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

1447
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni9 – 11Combined sources3
Beta strandi16 – 18Combined sources3
Beta strandi20 – 22Combined sources3
Beta strandi24 – 26Combined sources3
Helixi31 – 38Combined sources8
Beta strandi40 – 46Combined sources7
Helixi47 – 60Combined sources14
Helixi64 – 66Combined sources3
Beta strandi67 – 70Combined sources4
Helixi71 – 73Combined sources3
Helixi77 – 86Combined sources10
Beta strandi89 – 92Combined sources4
Helixi95 – 103Combined sources9
Helixi108 – 110Combined sources3
Beta strandi111 – 113Combined sources3
Helixi120 – 129Combined sources10
Beta strandi132 – 136Combined sources5
Helixi139 – 152Combined sources14
Beta strandi156 – 163Combined sources8
Beta strandi165 – 170Combined sources6
Beta strandi172 – 178Combined sources7
Beta strandi181 – 186Combined sources6
Turni187 – 190Combined sources4
Helixi191 – 201Combined sources11
Beta strandi203 – 211Combined sources9
Beta strandi215 – 218Combined sources4
Helixi222 – 246Combined sources25
Beta strandi252 – 254Combined sources3
Helixi272 – 289Combined sources18
Beta strandi296 – 299Combined sources4
Helixi303 – 306Combined sources4
Beta strandi310 – 323Combined sources14
Beta strandi325 – 327Combined sources3
Beta strandi329 – 336Combined sources8
Turni339 – 341Combined sources3
Helixi344 – 348Combined sources5
Beta strandi354 – 356Combined sources3
Beta strandi365 – 371Combined sources7
Beta strandi373 – 376Combined sources4
Beta strandi380 – 388Combined sources9
Beta strandi396 – 400Combined sources5
Beta strandi403 – 407Combined sources5
Helixi413 – 415Combined sources3
Beta strandi420 – 425Combined sources6
Beta strandi428 – 433Combined sources6
Helixi438 – 442Combined sources5

3D structure databases

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

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni300 – 303Pyridoxal phosphate bindingUniRule annotation1 Publication4

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

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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)DescriptionActionsGraphical viewLength
Sequence conflicti346A → G in AAA25361 (PubMed:8440471).Curated1
Sequence conflicti389 – 426DDIRP…VAVHA → TIFGPAIWLRLPPPALLLFA VESLQHGRPSRCGSGAR in AAA25361 (PubMed:8440471).CuratedAdd BLAST38

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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HKVX-ray2.60A/B1-447[»]
1HKWX-ray2.80A/B1-447[»]
2O0TX-ray2.33A/B/C/D2-447[»]
ProteinModelPortaliP9WIU7.
SMRiP9WIU7.
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.
BioCyciMTBH37RV:G185E-5467-MONOMER.
BRENDAi4.1.1.20. 3445.

Family and domain databases

CDDicd06828. PLPDE_III_DapDC. 1 hit.
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: November 2, 2016
This is version 19 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.