5ZLE

Human duodenal cytochrome b (Dcytb) in substrate free form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for promotion of duodenal iron absorption by enteric ferric reductase with ascorbate.

Ganasen, M.Togashi, H.Takeda, H.Asakura, H.Tosha, T.Yamashita, K.Hirata, K.Nariai, Y.Urano, T.Yuan, X.Hamza, I.Mauk, A.G.Shiro, Y.Sugimoto, H.Sawai, H.

(2018) Commun Biol 1: 120-120

  • DOI: https://doi.org/10.1038/s42003-018-0121-8
  • Primary Citation of Related Structures:  
    5ZLE, 5ZLG

  • PubMed Abstract: 

    Dietary iron absorption is regulated by duodenal cytochrome b (Dcytb), an integral membrane protein that catalyzes reduction of nonheme Fe 3+ by electron transfer from ascorbate across the membrane. This step is essential to enable iron uptake by the divalent metal transporter. Here we report the crystallographic structures of human Dcytb and its complex with ascorbate and Zn 2+ . Each monomer of the homodimeric protein possesses cytoplasmic and apical heme groups, as well as cytoplasmic and apical ascorbate-binding sites located adjacent to each heme. Zn 2+ coordinates to two hydroxyl groups of the apical ascorbate and to a histidine residue. Biochemical analysis indicates that Fe 3+ competes with Zn 2+ for this binding site. These results provide a structural basis for the mechanism by which Fe 3+ uptake is promoted by reducing agents and should facilitate structure-based development of improved agents for absorption of orally administered iron.


  • Organizational Affiliation

    Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori, Ako, Hyogo, 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b reductase 1292Homo sapiensMutation(s): 0 
Gene Names: CYBRD1DCYTBFRRS3
EC: 1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q53TN4 (Homo sapiens)
Explore Q53TN4 
Go to UniProtKB:  Q53TN4
PHAROS:  Q53TN4
GTEx:  ENSG00000071967 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53TN4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.45α = 90
b = 115.94β = 118.45
c = 48.43γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapanJP26220807
Japan Society for the Promotion of ScienceJapanJP24687015
Japan Society for the Promotion of ScienceJapanJP25871213

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-08-28
    Changes: Data collection
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description