3U2M | pdb_00003u2m

Crystal structure of human ALR mutant C142/145S

• PDB DOI: https://doi.org/10.2210/pdb3U2M/pdb

• Classification: FLAVOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-10-04 Released: 2012-06-06 
• Deposition Author(s): Banci, L., Bertini, I., Calderone, V., Cefaro, C., Ciofi-Baffoni, S., Gallo, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.291 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

An electron-transfer path through an extended disulfide relay system: the case of the redox protein ALR.

Banci, L., Bertini, I., Calderone, V., Cefaro, C., Ciofi-Baffoni, S., Gallo, A., Tokatlidis, K.

(2012) J Am Chem Soc 134: 1442-1445

• PubMed: 22224850 
• DOI: https://doi.org/10.1021/ja209881f
• Primary Citation Related Structures: 
  3U2L, 3U2M


• PubMed Abstract: 
  

  The oxidative folding mechanism in the intermembrane space of human mitochondria underpins a disulfide relay system consisting of the import receptor Mia40 and the homodimeric FAD-dependent thiol oxidase ALR. The flavoprotein ALR receives two electrons per subunit from Mia40, which are then donated through one-electron reactions to two cytochrome c molecules, thus mediating a switch from two-electron to one-electron transfer. We dissect here the mechanism of the electron flux within ALR, characterizing at the atomic level the ALR intermediates that allow electrons to rapidly flow to cytochrome c. The intermediate critical for the electron-transfer process implies the formation of a specific inter-subunit disulfide which exclusively allows electron flow from Mia40 to FAD. This finding allows us to present a complete model for the electron-transfer pathway in ALR.

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Organizational Affiliation: 
• Magnetic Resonance Center, University of Florence, via L. Sacconi 6, Sesto Fiorentino, Italy. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.47 kDa 
• Atom Count: 1,088 
• Modeled Residue Count: 115 
• Deposited Residue Count: 115 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FAD-linked sulfhydryl oxidase ALR	A	115	Homo sapiens	Mutation(s): 4  Gene Names: GFER, ALR, HERV1, HPO EC: 1.8.3.2
UniProt & NIH Common Fund Data Resources
Find proteins for P55789 (Homo sapiens) Explore P55789  Go to UniProtKB:  P55789
PHAROS:  P55789 GTEx:  ENSG00000127554

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.291 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.4	α = 90
b = 76.88	β = 90
c = 62.46	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Banci, L., Bertini, I., Calderone, V., Cefaro, C., Ciofi-Baffoni, S., Gallo, A.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary