3W6U

Crystal structure of NADP bound L-serine 3-dehydrogenase from Hyperthermophilic Archaeon Pyrobaculum calidifontis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 

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Literature

Crystal structure of the NADP+and tartrate-bound complex of L-serine 3-dehydrogenase from the hyperthermophilic archaeon Pyrobaculum calidifontis.

Yoneda, K.Sakuraba, H.Araki, T.Ohshima, T.

(2018) Extremophiles 22: 395-405

  • DOI: 10.1007/s00792-018-1004-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showe ...

    A gene encoding L-serine dehydrogenase (L-SerDH) that exhibits extremely low sequence identity to the Agrobacterium tumefaciens L-SerDH was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The predicted amino acid sequence showed 36% identity with that of Pseudomonas aeruginosa L-SerDH, suggesting that P. calidifontis L-SerDH is a novel type of L-SerDH, like Ps. aeruginosa L-SerDH. The overexpressed enzyme appears to be the most thermostable L-SerDH described to date, and no loss of activity was observed by incubation for 30 min at temperatures up to 100 °C. The enzyme showed substantial reactivity towards D-serine, in addition to L-serine. Two different crystal structures of P. calidifontis L-SerDH were determined using the Se-MAD and MR method: the structure in complex with NADP + /sulfate ion at 1.18 Å and the structure in complex with NADP + /L-tartrate (substrate analog) at 1.57 Å. The fold of the catalytic domain showed similarity with that of Ps. aeruginosa L-SerDH. However, the active site structure significantly differed between the two enzymes. Based on the structure of the tartrate, L- and D-serine and 3-hydroxypropionate molecules were modeled into the active site and the substrate binding modes were estimated. A structural comparison suggests that the wide cavity at the substrate binding site is likely responsible for the high reactivity of the enzyme toward both L- and D-serine enantiomers. This is the first description of the structure of the novel type of L-SerDH with bound NADP + and substrate analog, and it provides new insight into the substrate binding mechanism of L-SerDH. The results obtained here may be very informative for the creation of L- or D-serine-specific SerDH by protein engineering.


    Organizational Affiliation

    Department of Biomedical Engineering, Faculty of Engineering, Osaka Institute of Technology, 5-16-1 Ohmiya, Asahi-ku, Osaka, 535-8585, Japan.,Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Ikenobe 2393, Miki-cho, Kita-gun, Kagawa, 761-0795, Japan.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto, Kumamoto, 862-8652, Japan. kyoneda@agri.u-tokai.ac.jp.,Department of Bioscience, School of Agriculture, Tokai University, 9-1-1 Toroku, Higashi-ku, Kumamoto, Kumamoto, 862-8652, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphogluconate dehydrogenase, NAD-binding protein
A
306Pyrobaculum calidifontis (strain JCM 11548 / VA1)Mutation(s): 0 
Find proteins for A3MU08 (Pyrobaculum calidifontis (strain JCM 11548 / VA1))
Go to UniProtKB:  A3MU08
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 121.603α = 90.00
b = 56.827β = 106.69
c = 56.571γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data reduction
HKL-2000data collection
HKL-2000data scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2019-05-15
    Type: Data collection, Database references, Derived calculations