3IJP

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


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

  • 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 clo ...

    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 P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dihydrodipicolinate reductase
A, B
288Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)Mutation(s): 0 
Gene Names: dapB
EC: 1.17.1.8
Find proteins for Q6G2G3 (Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1))
Go to UniProtKB:  Q6G2G3
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NAP
Query on NAP

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A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
UNX
Query on UNX

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A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 109.380α = 90.00
b = 109.380β = 90.00
c = 176.950γ = 90.00
Software Package:
Software NamePurpose
BOSdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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