1YL6 | pdb_00001yl6

crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) (crystal form B)

• PDB DOI: https://doi.org/10.2210/pdb1YL6/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-01-19 Released: 2006-01-17 
• Deposition Author(s): Janowski, R., Kefala, G., Weiss, M.S., TB Structural Genomics Consortium (TBSGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.257 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.

Janowski, R., Kefala, G., Weiss, M.S.

(2010) Acta Crystallogr D Biol Crystallogr 66: 61-72

• PubMed: 20057050 
• DOI: https://doi.org/10.1107/S0907444909043960
• Primary Citation Related Structures: 
  1YL5, 1YL6, 1YL7


• PubMed Abstract: 
  

  Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.

---

Organizational Affiliation: 
• EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 51.46 kDa 
• Atom Count: 3,626 
• Modeled Residue Count: 490 
• Deposited Residue Count: 490 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrodipicolinate reductase	A, B	245	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dapB EC: 1.3.1.26 (PDB Primary Data), 1.17.1.8 (UniProt)
UniProt
Find proteins for P9WP23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP23  Go to UniProtKB:  P9WP23

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.257 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.13	α = 90
b = 89.46	β = 90
c = 77.52	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-01-17 
Deposition Author(s): Janowski, R., Kefala, G., Weiss, M.S., TB Structural Genomics Consortium (TBSGC)

Revision History  

• Version 1.0: 2006-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description