3TWO | pdb_00003two

The crystal structure of CAD from Helicobacter pylori complexed with NADP(H)

• PDB DOI: https://doi.org/10.2210/pdb3TWO/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Helicobacter pylori 51
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-22 Released: 2011-10-12 
• Deposition Author(s): Seo, K.H., Zhuang, N.N., Cong, C., Lee, K.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 
  0.226 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

Unusual NADPH conformation in the crystal structure of a cinnamyl alcohol dehydrogenase from Helicobacter pylori in complex with NADP(H) and substrate docking analysis

Seo, K.H., Zhuang, N.N., Chen, C., Song, J.Y., Kang, H.L., Rhee, K.H., Lee, K.H.

(2012) FEBS Lett 586: 337-343

• PubMed: 22269576 
• DOI: https://doi.org/10.1016/j.febslet.2012.01.020
• Primary Citation Related Structures: 
  3TWO


• PubMed Abstract: 
  

  Cinnamyl alcohol dehydrogenase is a zinc- and NADPH-dependent dehydrogenase catalyzing the reversible conversion of p-hydroxycinnamaldehydes to their corresponding hydroxycinnamyl alcohols. A CAD homolog from Helicobacter pylori (HpCAD) possesses broad substrate specificities like the plant CADs and additionally a dismutation activity converting benzaldehyde to benzyl alcohol and benzoic acid. We have determined the crystal structure of HpCAD complexed with NADP(H) at 2.18Å resolution to get a better understanding of this class of CAD outside of plants. The structure of HpCAD is highly homologous to the sinapyl alcohol dehydrogenase and the plant CAD with well-conserved residues involved in catalysis and zinc binding. However, the NADP(H) binding mode of the HpCAD has been found to be significantly different from those of plant CADs.

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Organizational Affiliation: 
• Division of Applied Life Science (BK21 Program), Gyeongsang National University, Jinju, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 79.23 kDa 
• Atom Count: 5,582 
• Modeled Residue Count: 695 
• Deposited Residue Count: 696 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannitol dehydrogenase	A, B	348	Helicobacter pylori 51	Mutation(s): 0  Gene Names: cad EC: 1.1.1.195

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	C [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
ZN	D [auth A], E [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free:  0.226 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.41	α = 90
b = 85.68	β = 90
c = 100.491	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-12 
Deposition Author(s): Seo, K.H., Zhuang, N.N., Cong, C., Lee, K.H.

Revision History  

• Version 1.0: 2011-10-12
  Type: Initial release
  
• Version 1.1: 2012-05-30
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description