3FVE | pdb_00003fve

Crystal structure of diaminopimelate epimerase Mycobacterium tuberculosis DapF

• PDB DOI: https://doi.org/10.2210/pdb3FVE/pdb

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


• Deposited: 2009-01-15 Released: 2009-01-27 
• Deposition Author(s): Usha, V., Dover, L.G., Roper, D.I., Futterer, K., Besra, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Structure of the diaminopimelate epimerase DapF from Mycobacterium tuberculosis

Usha, V., Dover, L.G., Roper, D.I., Futterer, K., Besra, G.S.

(2009) Acta Crystallogr D Biol Crystallogr 65: 383-387

• PubMed: 19307721 
• DOI: https://doi.org/10.1107/S0907444909002522
• Primary Citation Related Structures: 
  3FVE


• PubMed Abstract: 
  

  The meso (or D,L) isomer of diaminopimelic acid (DAP), a precursor of L-lysine, is a key component of the pentapeptide linker in bacterial peptidoglycan. While the peptidoglycan incorporated in the highly complex cell wall of the pathogen Mycobacterium tuberculosis structurally resembles that of Escherichia coli, it is unique in that it can contain penicillin-resistant meso-DAP-->meso-DAP linkages. The interconversion of L,L-DAP and meso-DAP is catalysed by the DAP epimerase DapF, a gene product that is essential in M. tuberculosis. Here, the crystal structure of the ligand-free form of M. tuberculosis DapF (MtDapF) refined to a resolution of 2.6 A is reported. MtDapF shows small if distinct deviations in secondary structure from the two-domain alpha/beta-fold of the known structures of Haemophilus influenzae DapF and Bacillus anthracis DapF, which are in line with its low sequence identity (

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Organizational Affiliation: 
• School of Biosciences, University of Birmingham, Edgbaston, Birmingham, England.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 30.2 kDa 
• Atom Count: 2,061 
• Modeled Residue Count: 283 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diaminopimelate epimerase	A	290	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: dapF, MT2798, MTCY154.06c, Rv2726c EC: 5.1.1.7
UniProt
Find proteins for P9WP19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WP19  Go to UniProtKB:  P9WP19

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	B [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.64	α = 90
b = 183.64	β = 90
c = 45.21	γ = 120

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-01-27 
Deposition Author(s): Usha, V., Dover, L.G., Roper, D.I., Futterer, K., Besra, G.S.

Revision History  

• Version 1.0: 2009-01-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description