3HRD

Crystal structure of nicotinate dehydrogenase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.224 

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This is version 1.2 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 U S A 106: 11055-11060

  • DOI: https://doi.org/10.1073/pnas.0902210106
  • Primary Citation of Related Structures:  
    3HRD

  • 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-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, Universität Bayreuth, 95440 Bayreuth, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinate dehydrogenase large molybdopterin subunit
A, E
425Eubacterium barkeriMutation(s): 0 
UniProt
Find proteins for Q0QLF2 (Eubacterium barkeri)
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Go to UniProtKB:  Q0QLF2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QLF2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinate dehydrogenase medium molybdopterin subunit
B, F
330Eubacterium barkeriMutation(s): 0 
UniProt
Find proteins for Q0QLF1 (Eubacterium barkeri)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QLF1
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinate dehydrogenase FAD-subunit
C, G
296Eubacterium barkeriMutation(s): 0 
UniProt
Find proteins for Q0QLF4 (Eubacterium barkeri)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QLF4
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Nicotinate dehydrogenase small FeS subunit
D, H
160Eubacterium barkeriMutation(s): 0 
UniProt
Find proteins for Q0QLF3 (Eubacterium barkeri)
Explore Q0QLF3 
Go to UniProtKB:  Q0QLF3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0QLF3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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P [auth C],
Z [auth G]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
MCN
Query on MCN

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N [auth B],
Y [auth F]
PTERIN CYTOSINE DINUCLEOTIDE
C19 H22 N8 O13 P2 S2
RBWYFPNWTRZKKZ-LOIMWUFNSA-N
FES
Query on FES

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AA [auth H],
BA [auth H],
R [auth D],
S [auth D]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
MOS
Query on MOS

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M [auth B],
X [auth F]
DIOXOTHIOMOLYBDENUM(VI) ION
H Mo O2 S
BDSRWPHSAKXXRG-UHFFFAOYSA-M
NIO
Query on NIO

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O [auth B],
U [auth E]
NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
SE
Query on SE

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I [auth A],
T [auth E]
SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
NO3
Query on NO3

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J [auth A],
Q [auth C],
V [auth E]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
CA
Query on CA

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W [auth E]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

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K [auth A],
L [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.069α = 90
b = 71.7β = 90.23
c = 214.485γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description