1YL7

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

Janowski, R.Kefala, G.Weiss, M.S.

(2010) Acta Crystallogr.,Sect.D 66: 61-72

  • DOI: 10.1107/S0907444909043960
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrodipicolinate reductase
A, B, C, D, E, F, G, H
245Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dapB
EC: 1.17.1.8
Find proteins for P9WP23 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WP23
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 238.600α = 90.00
b = 67.520β = 117.08
c = 154.490γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2013-10-30
    Type: Non-polymer description
  • Version 1.4: 2017-10-11
    Type: Refinement description