4V4E

Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with inhibitor 1,2,4,5-tetrahydroxy-benzene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of pyrogallol-phloroglucinol transhydroxylase, an Mo enzyme capable of intermolecular hydroxyl transfer between phenols

Messerschmidt, A.Niessen, H.Abt, D.Einsle, O.Schink, B.Kroneck, P.M.H.

(2004) Proc Natl Acad Sci U S A 101: 11571-11576

  • DOI: 10.1073/pnas.0404378101
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Mo enzyme transhydroxylase from the anaerobic microorganism Pelobacter acidigallici catalyzes the conversion of pyrogallol to phloroglucinol. Such trihydroxybenzenes and their derivatives represent important building blocks of plant polymers. Non ...

    The Mo enzyme transhydroxylase from the anaerobic microorganism Pelobacter acidigallici catalyzes the conversion of pyrogallol to phloroglucinol. Such trihydroxybenzenes and their derivatives represent important building blocks of plant polymers. None of the transferred hydroxyl groups originates from water during transhydroxylation; instead a cosubstrate, such as 1,2,3,5-tetrahydroxybenzene, is used in a reaction without apparent electron transfer. Here, we report on the crystal structure of the enzyme in the reduced Mo(IV) state, which we solved by single anomalous-diffraction technique. It represents the largest structure (1,149 amino acid residues per molecule, 12 independent molecules per unit cell), which has been solved so far by single anomalous-diffraction technique. Tranhydroxylase is a heterodimer, with the active Mo-molybdopterin guanine dinucleotide (MGD)(2) site in the alpha-subunit, and three [4Fe-4S] centers in the beta-subunit. The latter subunit carries a seven-stranded, mainly antiparallel beta-barrel domain. We propose a scheme for the transhydroxylation reaction based on 3D structures of complexes of the enzyme with various polyphenols serving either as substrate or inhibitor.


    Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18, 82152 Martinsried, Germany.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyrogallol hydroxytransferase large subunitA, C, E, G, I, K, M, O, Q, S, U, W875Pelobacter acidigalliciMutation(s): 0 
Gene Names: athL
EC: 1.97.1.2
Find proteins for P80563 (Pelobacter acidigallici)
Explore P80563 
Go to UniProtKB:  P80563
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pyrogallol hydroxytransferase small subunitB, D, F, H, J, L, N, P, R, T, V, X274Pelobacter acidigalliciMutation(s): 0 
Gene Names: bthL
EC: 1.97.1.2
Find proteins for P80564 (Pelobacter acidigallici)
Explore P80564 
Go to UniProtKB:  P80564
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download CCD File 
A, C, E, G, I, K, M, O, Q, S, U, W
2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
 Ligand Interaction
SF4
Query on SF4

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B, D, F, H, J, L, N, P, R, T, V, X
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
BTT
Query on BTT

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A, C, E, G, I, K, M, O, Q, S, U, W
BENZENE-1,2,4,5-TETROL
C6 H6 O4
UYQMSQMCIYSXOW-UHFFFAOYSA-N
 Ligand Interaction
4MO
Query on 4MO

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A, C, E, G, I, K, M, O, Q, S, U, W
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.575α = 63.83
b = 178.437β = 64.4
c = 179.665γ = 65.04
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other