Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

Experimental Data Snapshot

  • Resolution: 2.28 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 

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This is version 1.3 of the entry. See complete history


Crystal structure and kinetic study of dihydrodipicolinate synthase from Mycobacterium tuberculosis.

Kefala, G.Evans, G.L.Griffin, M.D.Devenish, S.R.Pearce, F.G.Perugini, M.A.Gerrard, J.A.Weiss, M.S.Dobson, R.C.

(2008) Biochem J 411: 351-360

  • DOI: https://doi.org/10.1042/BJ20071360
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The three-dimensional structure of the enzyme dihydrodipicolinate synthase (KEGG entry Rv2753c, EC from Mycobacterium tuberculosis (Mtb-DHDPS) was determined and refined at 2.28 A (1 A=0.1 nm) resolution. The asymmetric unit of the crystal contains two tetramers, each of which we propose to be the functional enzyme unit. This is supported by analytical ultracentrifugation studies, which show the enzyme to be tetrameric in solution. The structure of each subunit consists of an N-terminal (beta/alpha)(8)-barrel followed by a C-terminal alpha-helical domain. The active site comprises residues from two adjacent subunits, across an interface, and is located at the C-terminal side of the (beta/alpha)(8)-barrel domain. A comparison with the other known DHDPS structures shows that the overall architecture of the active site is largely conserved, albeit the proton relay motif comprising Tyr(143), Thr(54) and Tyr(117) appears to be disrupted. The kinetic parameters of the enzyme are reported: K(M)(ASA)=0.43+/-0.02 mM, K(M)(pyruvate)=0.17+/-0.01 mM and V(max)=4.42+/-0.08 micromol x s(-1) x mg(-1). Interestingly, the V(max) of Mtb-DHDPS is 6-fold higher than the corresponding value for Escherichia coli DHDPS, and the enzyme is insensitive to feedback inhibition by (S)-lysine. This can be explained by the three-dimensional structure, which shows that the (S)-lysine-binding site is not conserved in Mtb-DHDPS, when compared with DHDPS enzymes that are known to be inhibited by (S)-lysine. A selection of metabolites from the aspartate family of amino acids do not inhibit this enzyme. A comprehensive understanding of the structure and function of this important enzyme from the (S)-lysine biosynthesis pathway may provide the key for the design of new antibiotics to combat tuberculosis.

  • Organizational Affiliation

    EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydrodipicolinate synthase
A, B, C, D, E
A, B, C, D, E, F, G, H
303Mycobacterium tuberculosisMutation(s): 0 
Gene Names: dapA
Find proteins for P9WP25 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WP25 
Go to UniProtKB:  P9WP25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WP25
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on DTT

Download Ideal Coordinates CCD File 
CA [auth G]
FA [auth H]
K [auth A]
N [auth B]
Q [auth C]
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
C4 H10 O2 S2
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
EA [auth H]
J [auth A]
M [auth B]
P [auth C]
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
Query on MG

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.28 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.149 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.79α = 90
b = 87.37β = 107.78
c = 139.85γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description