2YXG | pdb_00002yxg

Crystal structure of Dihyrodipicolinate Synthase (dapA)

• PDB DOI: https://doi.org/10.2210/pdb2YXG/pdb

• Classification: LYASE
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-04-26 Released: 2007-10-30 
• Deposition Author(s): Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.224 (Depositor) 
• R-Value Work: 
  0.158 (Depositor) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Structure of dihydrodipicolinate synthase from Methanocaldococcus jannaschii.

Padmanabhan, B., Strange, R.W., Antonyuk, S.V., Ellis, M.J., Hasnain, S.S., Iino, H., Agari, Y., Bessho, Y., Yokoyama, S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1222-1226

• PubMed: 20054116 
• DOI: https://doi.org/10.1107/S174430910904651X
• Primary Citation Related Structures: 
  2YXG


• PubMed Abstract: 
  

  In bacteria and plants, dihydrodipicolinate synthase (DHDPS) plays a key role in the (S)-lysine biosynthesis pathway. DHDPS catalyzes the first step of the condensation of (S)-aspartate-beta-semialdehyde and pyruvate to form an unstable compound, (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid. The activity of DHDPS is allosterically regulated by (S)-lysine, a feedback inhibitor. The crystal structure of DHDPS from Methanocaldococcus jannaschii (MjDHDPS) was solved by the molecular-replacement method and was refined to 2.2 A resolution. The structure revealed that MjDHDPS forms a functional homotetramer, as also observed in Escherichia coli DHDPS, Thermotoga maritima DHDPS and Bacillus anthracis DHDPS. The binding-site region of MjDHDPS is essentially similar to those found in other known DHDPS structures.

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Organizational Affiliation: 
• Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama 230-0045, Japan. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 126.45 kDa 
• Atom Count: 9,549 
• Modeled Residue Count: 1,153 
• Deposited Residue Count: 1,156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate synthase	A, B, C, D	289	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 0  Gene Names: dapA EC: 4.2.1.52 (PDB Primary Data), 4.3.3.7 (UniProt)
UniProt
Find proteins for Q57695 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57695  Go to UniProtKB:  Q57695

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.224 (Depositor) 
• R-Value Work:  0.158 (Depositor) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.469	α = 90
b = 76.532	β = 106.87
c = 101.863	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-30 
Deposition Author(s): Padmanabhan, B., Bessho, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2007-10-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Refinement description