1RM6

Structure of 4-hydroxybenzoyl-CoA reductase from Thauera aromatica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a Xanthine Oxidase-Related 4-Hydroxybenzoyl-CoA Reductase with an Additional [4Fe-4S] Cluster and an Inverted Electron Flow

Unciuleac, M.Warkentin, E.Page, C.C.Boll, M.Ermler, U.

(2004) Structure 12: 2249-2256

  • DOI: https://doi.org/10.1016/j.str.2004.10.008
  • Primary Citation of Related Structures:  
    1RM6, 1SB3

  • PubMed Abstract: 
  • The Mo-flavo-Fe/S-dependent heterohexameric protein complex 4-hydroxybenzoyl-CoA reductase (4-HBCR, dehydroxylating) is a central enzyme of the anaerobic degradation of phenolic compounds and belongs to the xanthine oxidase (XO) family of molybdenum enzymes ...

    The Mo-flavo-Fe/S-dependent heterohexameric protein complex 4-hydroxybenzoyl-CoA reductase (4-HBCR, dehydroxylating) is a central enzyme of the anaerobic degradation of phenolic compounds and belongs to the xanthine oxidase (XO) family of molybdenum enzymes. Its X-ray structure was established at 1.6 A resolution. The most pronounced difference between 4-HBCR and other structurally characterized members of the XO family is the insertion of 40 amino acids within the beta subunit, which carries an additional [4Fe-4S] cluster at a distance of 16.5 A to the isoalloxazine ring of FAD. The architecture of 4-HBCR and concomitantly performed electron transfer rate calculations suggest an inverted electron transfer chain from the donor ferredoxin via the [4Fe-4S] cluster to the Mo over a distance of 55 A. The binding site of 4-hydroxybenzoyl-CoA is located in an 18 A long channel lined up by several aromatic side chains around the aromatic moiety, which are proposed to shield and stabilize the postulated radical intermediates during catalysis.


    Organizational Affiliation

    Institut für Biologie II, Mikrobiologie Schänzlestrasse 1, D-79104 Freiburg, Germany.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxybenzoyl-CoA reductase alpha subunitA, D769Thauera aromaticaMutation(s): 0 
Gene Names: hcrA
EC: 1.3.99.20 (PDB Primary Data), 1.1.7.1 (UniProt)
UniProt
Find proteins for O33819 (Thauera aromatica)
Explore O33819 
Go to UniProtKB:  O33819
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33819
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxybenzoyl-CoA reductase beta subunitB, E324Thauera aromaticaMutation(s): 0 
Gene Names: hcrB
EC: 1.3.99.20 (PDB Primary Data), 1.1.7.1 (UniProt)
UniProt
Find proteins for O33820 (Thauera aromatica)
Explore O33820 
Go to UniProtKB:  O33820
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33820
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
4-hydroxybenzoyl-CoA reductase gamma subunitC, F161Thauera aromaticaMutation(s): 0 
Gene Names: hcrC
EC: 1.3.99.20 (PDB Primary Data), 1.1.7.1 (UniProt)
UniProt
Find proteins for O33818 (Thauera aromatica)
Explore O33818 
Go to UniProtKB:  O33818
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO33818
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCD
Query on PCD

Download Ideal Coordinates CCD File 
I [auth A],
U [auth D]
(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
C19 H26 Mo N8 O16 P2 S2
YEBYDVFRFUQMER-NBXMTLLYDD
 Ligand Interaction
FAD
Query on FAD

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M [auth B],
W [auth E]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SF4
Query on SF4

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N [auth B],
X [auth E]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
EPE
Query on EPE

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A],
V [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
FES
Query on FES

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O [auth C],
P [auth C],
Y [auth F],
Z [auth F]
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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T [auth D]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
K
Query on K

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R [auth D]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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G [auth A],
Q [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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H [auth A],
S [auth D]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.015α = 90
b = 151.845β = 90
c = 174.866γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-21
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance