Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 195.66 kDa 
• Atom Count: 15128 
• Modelled Residue Count: 1736 
• Deposited Residue Count: 1736 
• Unique protein chains: 1

1TWI

Crystal structure of Diaminopimelate Decarboxylase from m. jannaschii in co-complex with L-lysine

• DOI: 10.2210/pdb1TWI/pdb

• Classification: LYASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-07-01 Released: 2004-07-27 
• Deposition Author(s): Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M.G., He, G., De Lencastre, H., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 

Literature

Cocrystal structures of diaminopimelate decarboxylase: mechanism, evolution, and inhibition of an antibiotic resistance accessory factor

Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M.G., He, G., De Lencastre, H., Tomasz, A., Burley, S.K.

(2002) Structure 10: 1499-1508

• PubMed: 12429091 
• DOI: 10.1016/s0969-2126(02)00880-8
• Primary Citation of Related Structures:  
  1TUF, 1TWI


• PubMed Abstract: 
  

Cocrystal structures of Methanococcus jannaschii diaminopimelate decarboxylase (DAPDC) bound to a substrate analog, azelaic acid, and its L-lysine product have been determined at 2.6 A and 2.0 A, respectively. This PLP-dependent enzyme is responsible for the final step of L-lysine biosynthesis in bacteria and plays a role in beta-lactam antibiotic resistance in Staphylococcus aureus. Substrate specificity derives from recognition of the L-chiral center of diaminopimelate and a system of ionic "molecular rulers" that dictate substrate length. A coupled-enzyme assay system permitted measurement of kinetic parameters for recombinant DAPDCs and inhibition constants (K(i)) for azelaic acid (89 microM) and other substrate analogs. Implications for rational design of broad-spectrum antimicrobial agents targeted against DAPDCs of drug-resistant strains of bacterial pathogens, such as Staphylococcus aureus, are discussed.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate decarboxylase	A, B, C, D	434	Methanocaldococcus jannaschii	Mutation(s): 0  Gene Names: lysA, MJ1097 EC: 4.1.1.20
UniProt
Find proteins for Q58497 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58497  Go to UniProtKB:  Q58497

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP (Subject of Investigation/LOI)	E [auth A], F [auth B], H [auth C], O [auth D]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
LYS	I [auth D], J [auth D], K [auth D], L [auth D], M [auth D], N [auth D]	LYSINE C6 H15 N2 O2 KDXKERNSBIXSRK-YFKPBYRVSA-O
MG	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.202 
• R-Value Work: 0.157 
• R-Value Observed: 0.157 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.242	α = 90
b = 147.07	β = 97.25
c = 89.389	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2004-07-01 
• Released Date: 2004-07-27 
Deposition Author(s): Rajashankar, K.R., Ray, S.S., Bonanno, J.B., Pinho, M.G., He, G., De Lencastre, H., Tomasz, A., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-07-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary