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 

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 U S A 106: 11055-11060

  • DOI: 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-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, Universität Bayreuth, 95440 Bayreuth, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinate dehydrogenase large molybdopterin subunitA, E425Eubacterium barkeriMutation(s): 0 
Gene Names: ndhL
EC: 1.17.1.5
Find proteins for Q0QLF2 (Eubacterium barkeri)
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Go to UniProtKB:  Q0QLF2
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinate dehydrogenase FAD-subunitC, G296Eubacterium barkeriMutation(s): 0 
Gene Names: ndhF
EC: 1.17.1.5
Find proteins for Q0QLF4 (Eubacterium barkeri)
Explore Q0QLF4 
Go to UniProtKB:  Q0QLF4
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinate dehydrogenase small FeS subunitD, H160Eubacterium barkeriMutation(s): 0 
Gene Names: ndhS
EC: 1.17.1.5
Find proteins for Q0QLF3 (Eubacterium barkeri)
Explore Q0QLF3 
Go to UniProtKB:  Q0QLF3
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nicotinate dehydrogenase medium molybdopterin subunitB, F330Eubacterium barkeriMutation(s): 0 
Gene Names: ndhM
EC: 1.17.1.5
Find proteins for Q0QLF1 (Eubacterium barkeri)
Explore Q0QLF1 
Go to UniProtKB:  Q0QLF1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

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C, G
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
MCN
Query on MCN

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

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D, H
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
MOS
Query on MOS

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

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B, E
NICOTINIC ACID
C6 H5 N O2
PVNIIMVLHYAWGP-UHFFFAOYSA-N
 Ligand Interaction
SE
Query on SE

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A, E
SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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A, C, E
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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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Entry History 

Deposition Data

Revision History 

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