1HKV Lyase date Mar 11, 2003
title Mycobacterium Diaminopimelate Dicarboxylase (Lysa)
authors K.Gokulan, B.Rupp, M.S.Pavelka Junior, W.R.Jacobs Junior, J.C.Sacchettini, Tb Structural Genomics Consortium (Tb)
compound source
Molecule: Diaminopimelate Decarboxylase
Synonym: Dap Decarboxylase,Meso-Diaminopimelate Decarboxylase,Lysa;
Ec: 4.1.1.20
Chain: A, B
Engineered: Yes
Other_details: Complexed With Cofactor Plp And Product Lysine
 Organism_scientific: Mycobacterium Tuberculosis
Strain: H37rv
Expression_system: Escherichia Coli
Expression_system_strain: B834(De3) Met-
Expression_system_vector: Pet30bhis
Other_details: C-Term 6-His Tag
symmetry Space Group: P 41 21 2
R_factor 0.22437
crystal
cell
length a length b length c angle alpha angle beta angle gamma
111.452 111.452 238.253 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.6 Å
ligand LYS, PLP enzyme Diaminopimelate decarboxylase;. Diaminopimelic acid decarboxylase;. Meso-diaminopimelate decarboxylase;. DAP-decarboxylase. Lyase E.C.4.1.1.20 BRENDA
note 1HKV is a representative structure
similarity Belongs to the orn/lys/arg decarboxylase class-ii family.[Orn_DAP_Arg_deC]
catalytic activ. Meso-2,6-diaminoheptanedioate = l-lysine + co(2).
pathway Amino-acid biosynthesis; l-lysine biosynthesis via dap pathway; l-lysine from dl-diaminopimelate: single step [final step].
genes lysA (E. coli); lysA (M. jannaschii); MT1332, lysA (M. tuberculosis)
Primary referenceCrystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis., Gokulan K, Rupp B, Pavelka MS Jr, Jacobs WR Jr, Sacchettini JC, J Biol Chem 2003 May 16;278(20):18588-96. PMID:12637582
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (1hkv.pdb1.gz) 141 Kb
  • CSU: Contacts of Structural Units for 1HKV
  • Likely Quarternary Molecular Structure file(s) for 1HKV
  • Structure Factors (371 Kb)
  • Retrieve 1HKV in mmCIF format [Save to disk]
    • View 1HKV in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
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    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1HKV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1hkva1, region A:2-45,A:311-447 [Jmol] [rasmolscript] [script source]
        - Domain d1hkva2, region A:46-310 [Jmol] [rasmolscript] [script source]
        - Domain d1hkvb1, region B:2-45,B:311-447 [Jmol] [rasmolscript] [script source]
        - Domain d1hkvb2, region B:46-310 [Jmol] [rasmolscript] [script source]
  • Fold representative 1hkv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1hkv_A] [1hkv_B]
    • Other resources with information on 1HKV
  • InterPro: IPR002986 , IPR000183
  • MMDB (Entrez's Structure Database)
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