5A4R | pdb_00005a4r

Crystal structure of a vitamin B12 trafficking protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.255 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.229 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5A4R

This is version 1.3 of the entry. See complete history

Literature

Structural Insights Into the Mmachc-Mmadhc Protein Complex Involved in Vitamin B12 Trafficking.

Froese, D.S.Kopec, J.Fitzpatrick, F.Schuller, M.Mccorvie, T.J.Chalk, R.Plessl, T.Fettelschoss, V.Fowler, B.Baumgartner, M.R.Yue, W.W.

(2015) J Biological Chem 290: 29167

  • DOI: https://doi.org/10.1074/jbc.M115.683268
  • Primary Citation Related Structures: 
    5A4R

  • PubMed Abstract: 

    Conversion of vitamin B12 (cobalamin, Cbl) into the cofactor forms methyl-Cbl (MeCbl) and adenosyl-Cbl (AdoCbl) is required for the function of two crucial enzymes, mitochondrial methylmalonyl-CoA mutase and cytosolic methionine synthase, respectively. The intracellular proteins MMACHC and MMADHC play important roles in processing and targeting the Cbl cofactor to its destination enzymes, and recent evidence suggests that they may interact while performing these essential trafficking functions. To better understand the molecular basis of this interaction, we have mapped the crucial protein regions required, indicate that Cbl is likely processed by MMACHC prior to interaction with MMADHC, and identify patient mutations on both proteins that interfere with complex formation, via different mechanisms. We further report the crystal structure of the MMADHC C-terminal region at 2.2 Å resolution, revealing a modified nitroreductase fold with surprising homology to MMACHC despite their poor sequence conservation. Because MMADHC demonstrates no known enzymatic activity, we propose it as the first protein known to repurpose the nitroreductase fold solely for protein-protein interaction. Using small angle x-ray scattering, we reveal the MMACHC-MMADHC complex as a 1:1 heterodimer and provide a structural model of this interaction, where the interaction region overlaps with the MMACHC-Cbl binding site. Together, our findings provide novel structural evidence and mechanistic insight into an essential biological process, whereby an intracellular "trafficking chaperone" highly specific for a trace element cofactor functions via protein-protein interaction, which is disrupted by inherited disease mutations.


  • Organizational Affiliation
    • From the Division of Metabolism and Children's Research Center, University Children's, Hospital, CH-8032 Zurich, Switzerland, radiz - Rare Disease Initiative Zurich, Clinical Research Priority Program for Rare Diseases, University of Zurich, CH-8032 Zurich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 19.22 kDa 
  • Atom Count: 1,144 
  • Modeled Residue Count: 148 
  • Deposited Residue Count: 170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, MITOCHONDRIAL170Mus musculusMutation(s): 0 
UniProt
Find proteins for Q99LS1 (Mus musculus)
Explore Q99LS1 
Go to UniProtKB:  Q99LS1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99LS1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.229 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.21α = 90
b = 89.53β = 90
c = 64.67γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-28
    Type: Initial release
  • Version 1.1: 2015-11-04
    Changes: Database references
  • Version 1.2: 2015-12-16
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Other