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Link to original content: https://www.rcsb.org/structure/4V4D
RCSB PDB - 4V4D: Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with pyrogallol

 4V4D

Crystal Structure of Pyrogallol-Phloroglucinol Transhydroxylase from Pelobacter acidigallici complexed with pyrogallol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1073/pnas.0404378101
  • Primary Citation of Related Structures:  
    4V4C, 4V4D, 4V4E

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrogallol hydroxytransferase large subunit
A, C, E, G, I
A, C, E, G, I, K, M, O, Q, S, U, W
875Pelobacter acidigalliciMutation(s): 0 
EC: 1.97.1.2
UniProt
Find proteins for P80563 (Pelobacter acidigallici)
Explore P80563 
Go to UniProtKB:  P80563
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80563
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Pyrogallol hydroxytransferase small subunit
B, D, F, H, J
B, D, F, H, J, L, N, P, R, T, V, X
274Pelobacter acidigalliciMutation(s): 0 
EC: 1.97.1.2
UniProt
Find proteins for P80564 (Pelobacter acidigallici)
Explore P80564 
Go to UniProtKB:  P80564
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80564
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MGD
Query on MGD

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth G]
AC [auth M]
BB [auth G]
BC [auth M]
AA [auth A],
AB [auth G],
AC [auth M],
BB [auth G],
BC [auth M],
BD [auth S],
CD [auth S],
IA [auth C],
JA [auth C],
JB [auth I],
JC [auth O],
KB [auth I],
KC [auth O],
KD [auth U],
LD [auth U],
RA [auth E],
RB [auth K],
SA [auth E],
SB [auth K],
SC [auth Q],
TC [auth Q],
TD [auth W],
UD [auth W],
Z [auth A]
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
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AE [auth X]
EA [auth B]
FA [auth B]
FB [auth H]
FC [auth N]
AE [auth X],
EA [auth B],
FA [auth B],
FB [auth H],
FC [auth N],
GA [auth B],
GB [auth H],
GC [auth N],
GD [auth T],
HB [auth H],
HC [auth N],
HD [auth T],
ID [auth T],
NA [auth D],
NB [auth J],
OA [auth D],
OB [auth J],
OC [auth P],
PA [auth D],
PB [auth J],
PC [auth P],
PD [auth V],
QC [auth P],
QD [auth V],
RD [auth V],
WA [auth F],
WB [auth L],
XA [auth F],
XB [auth L],
XC [auth R],
YA [auth F],
YB [auth L],
YC [auth R],
YD [auth X],
ZC [auth R],
ZD [auth X]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
PYG
Query on PYG

Download Ideal Coordinates CCD File 
CA [auth A]
DB [auth G]
DC [auth M]
ED [auth S]
LA [auth C]
CA [auth A],
DB [auth G],
DC [auth M],
ED [auth S],
LA [auth C],
MB [auth I],
MC [auth O],
ND [auth U],
UA [auth E],
UB [auth K],
VC [auth Q],
WD [auth W]
BENZENE-1,2,3-TRIOL
C6 H6 O3
WQGWDDDVZFFDIG-UHFFFAOYSA-N
4MO
Query on 4MO

Download Ideal Coordinates CCD File 
BA [auth A]
CB [auth G]
CC [auth M]
DD [auth S]
KA [auth C]
BA [auth A],
CB [auth G],
CC [auth M],
DD [auth S],
KA [auth C],
LB [auth I],
LC [auth O],
MD [auth U],
TA [auth E],
TB [auth K],
UC [auth Q],
VD [auth W]
MOLYBDENUM(IV) ION
Mo
ZIKKVZAYJJZBGE-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AD [auth S]
DA [auth B]
EB [auth H]
EC [auth N]
FD [auth T]
AD [auth S],
DA [auth B],
EB [auth H],
EC [auth N],
FD [auth T],
HA [auth C],
IB [auth I],
IC [auth O],
JD [auth U],
MA [auth D],
NC [auth P],
OD [auth V],
QA [auth E],
QB [auth K],
RC [auth Q],
SD [auth W],
VA [auth F],
VB [auth L],
WC [auth R],
XD [auth X],
Y [auth A],
ZA [auth G],
ZB [auth M]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.473α = 64.11
b = 178.14β = 64.45
c = 179.05γ = 65.11
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description