3HRD

Crystal structure of nicotinate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Mo-Se active site of nicotinate dehydrogenase

Wagener, N.Pierik, A.J.Ibdah, A.Hille, R.Dobbek, H.

(2009) Proc.Natl.Acad.Sci.USA 106: 11055-11060

  • DOI: 10.1073/pnas.0902210106

  • PubMed Abstract: 
  • Nicotinate dehydrogenase (NDH) from Eubacterium barkeri is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. Reactivity of NDH critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-u ...

    Nicotinate dehydrogenase (NDH) from Eubacterium barkeri is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. Reactivity of NDH critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-unidentified form and function. We have determined the crystal structure of NDH and analyzed its active site by multiple wavelengths anomalous dispersion methods. We show that selenium is bound as a terminal Mo=Se ligand to molybdenum and that it occupies the position of the terminal sulfido ligand in other molybdenum hydroxylases. The role of selenium in catalysis has been assessed by model calculations, which indicate an acceleration of the critical hydride transfer from the substrate to the selenido ligand in the course of substrate hydroxylation when compared with an active site containing a sulfido ligand. The MoO(OH)Se active site of NDH shows a novel type of utilization and reactivity of selenium in nature.


    Organizational Affiliation

    Bioanorganische Chemie, Universit├Ąt Bayreuth, 95440 Bayreuth, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nicotinate dehydrogenase large molybdopterin subunit
A, E
425Eubacterium barkeriMutation(s): 0 
Gene Names: ndhL
EC: 1.17.1.5
Find proteins for Q0QLF2 (Eubacterium barkeri)
Go to UniProtKB:  Q0QLF2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nicotinate dehydrogenase medium molybdopterin subunit
B, F
330Eubacterium barkeriMutation(s): 0 
Gene Names: ndhM
EC: 1.17.1.5
Find proteins for Q0QLF1 (Eubacterium barkeri)
Go to UniProtKB:  Q0QLF1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nicotinate dehydrogenase FAD-subunit
C, G
296Eubacterium barkeriMutation(s): 0 
Gene Names: ndhF
EC: 1.17.1.5
Find proteins for Q0QLF4 (Eubacterium barkeri)
Go to UniProtKB:  Q0QLF4
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Nicotinate dehydrogenase small FeS subunit
D, H
160Eubacterium barkeriMutation(s): 0 
Gene Names: ndhS
EC: 1.17.1.5
Find proteins for Q0QLF3 (Eubacterium barkeri)
Go to UniProtKB:  Q0QLF3
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NIO
Query on NIO

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Download CCD File 
B, E
NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
 Ligand Interaction
MCN
Query on MCN

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Download CCD File 
B, F
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
C, G
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
CA
Query on CA

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E
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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Download CCD File 
D, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SE
Query on SE

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A, E
SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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Download CCD File 
B, F
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A, C, E
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 97.069α = 90.00
b = 71.700β = 90.23
c = 214.485γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
AMoREphasing
XDSdata reduction
MAR345dtbdata collection
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance