1ZPU | pdb_00001zpu

Crystal Structure of Fet3p, a Multicopper Oxidase that Functions in Iron Import


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.257 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.226 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

The copper-iron connection in biology: Structure of the metallo-oxidase Fet3p.

Taylor, A.B.Stoj, C.S.Ziegler, L.Kosman, D.J.Hart, P.J.

(2005) Proc Natl Acad Sci U S A 102: 15459-15464

  • DOI: https://doi.org/10.1073/pnas.0506227102
  • Primary Citation Related Structures: 
    1ZPU

  • PubMed Abstract: 

    Fet3p is a multicopper-containing glycoprotein localized to the yeast plasma membrane that catalyzes the oxidation of Fe(II) to Fe(III). This ferrous iron oxidation is coupled to the reduction of O(2) to H(2)O and is termed the ferroxidase reaction. Fet3p-produced Fe(III) is transferred to the permease Ftr1p for import into the cytosol. The posttranslational insertion of four copper ions into Fet3p is essential for its activity, thus linking copper and iron homeostasis. The mammalian ferroxidases ceruloplasmin and hephaestin are homologs of Fet3p. Loss of the Fe(II) oxidation catalyzed by these proteins results in a spectrum of pathological states, including death. Here, we present the structure of the Fet3p extracellular ferroxidase domain and compare it with that of human ceruloplasmin and other multicopper oxidases that are devoid of ferroxidase activity. The Fet3p structure delineates features that underlie the unique reactivity of this and homologous multicopper oxidases that support the essential trafficking of iron in diverse eukaryotic organisms. The findings are correlated with biochemical and physiological data to cross-validate the elements of Fet3p that define it as both a ferroxidase and cuprous oxidase.


  • Organizational Affiliation
    • Department of Biochemistry and the X-Ray Crystallography Core Laboratory, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, USA.

Macromolecule Content 

  • Total Structure Weight: 398.63 kDa 
  • Atom Count: 27,659 
  • Modeled Residue Count: 3,174 
  • Deposited Residue Count: 3,204 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Iron transport multicopper oxidase FET3
A, B, C, D, E
A, B, C, D, E, F
534Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FET3
EC: 1 (PDB Primary Data), 1.16.3.1 (UniProt), 1.16.3.4 (UniProt)
UniProt
Find proteins for P38993 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38993 
Go to UniProtKB:  P38993
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38993
Glycosylation
Glycosylation Sites: 10Go to GlyGen: P38993-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
AA [auth a],
DA [auth d],
FA [auth f],
G,
IA [auth i],
AA [auth a],
DA [auth d],
FA [auth f],
G,
IA [auth i],
J,
KA [auth k],
M,
O,
S,
U,
Y
5N-Glycosylation
Glycosylation Resources
GlyTouCan: G22768VO
GlyCosmos: G22768VO
GlyGen: G22768VO
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH,
JA [auth j],
N,
Z
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G09724ZC
GlyCosmos: G09724ZC
GlyGen: G09724ZC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
GA [auth g],
I,
P,
Q,
BA [auth b],
GA [auth g],
I,
P,
Q,
V
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
CA [auth c],
HA [auth h],
K,
L,
LA [auth l],
CA [auth c],
HA [auth h],
K,
L,
LA [auth l],
W,
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 6
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
R
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 7
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseEA [auth e],
T
7N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL
GlyCosmos: G55220VL
GlyGen: G55220VL

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AC [auth E]
EB [auth C]
FB [auth C]
FC [auth F]
GB [auth C]
AC [auth E],
EB [auth C],
FB [auth C],
FC [auth F],
GB [auth C],
GC [auth F],
HB [auth C],
HC [auth F],
IB [auth C],
IC [auth F],
JC [auth F],
KC [auth F],
MA [auth A],
NA [auth A],
NB [auth D],
OA [auth A],
OB [auth D],
PA [auth A],
PB [auth D],
QA [auth A],
QB [auth D],
RB [auth D],
VA [auth B],
WA [auth B],
WB [auth E],
XA [auth B],
XB [auth E],
YA [auth B],
YB [auth E],
ZA [auth B],
ZB [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
CU1

Query on CU1



Download:Ideal Coordinates CCD File
AB [auth B]
BB [auth B]
BC [auth E]
CB [auth B]
CC [auth E]
AB [auth B],
BB [auth B],
BC [auth E],
CB [auth B],
CC [auth E],
DB [auth B],
DC [auth E],
EC [auth E],
JB [auth C],
KB [auth C],
LB [auth C],
LC [auth F],
MB [auth C],
MC [auth F],
NC [auth F],
OC [auth F],
RA [auth A],
SA [auth A],
SB [auth D],
TA [auth A],
TB [auth D],
UA [auth A],
UB [auth D],
VB [auth D]
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.257 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.226 (Depositor), 0.235 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.534α = 90
b = 168.534β = 90
c = 174.605γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-10-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary