3IJP

Crystal structure of dihydrodipicolinate reductase from bartonella henselae at 2.0A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 1.4 of the entry. See complete history


Literature

The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 angstrom resolution.

Cala, A.R.Nadeau, M.T.Abendroth, J.Staker, B.L.Reers, A.R.Weatherhead, A.W.Dobson, R.C.Myler, P.J.Hudson, A.O.

(2016) Acta Crystallogr F Struct Biol Commun 72: 885-891

  • DOI: 10.1107/S2053230X16018525
  • Primary Citation of Related Structures:  
    3IJP

  • PubMed Abstract: 
  • In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported ...

    In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4 3 22, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. R r.i.m. was 0.11, R work was 0.177 and R free was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP + was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.


    Organizational Affiliation

    Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623-5603, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydrodipicolinate reductaseA, B288Bartonella henselaeMutation(s): 0 
Gene Names: dapBBH12440
EC: 1.3.1.26 (PDB Primary Data), 1.17.1.8 (UniProt)
UniProt
Find proteins for Q6G2G3 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1))
Explore Q6G2G3 
Go to UniProtKB:  Q6G2G3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.38α = 90
b = 109.38β = 90
c = 176.95γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-12-14
    Changes: Database references
  • Version 1.3: 2017-01-25
    Changes: Database references
  • Version 1.4: 2017-02-01
    Changes: Database references, Structure summary