Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 112401.06 
• Atom Count: 7652 
• Residue Count: 994 
• Unique protein chains: 1

2BRY

Crystal structure of the native monooxygenase domain of MICAL at 1.45 A resolution

• DOI: 10.2210/pdb2BRY/pdb

• Classification: TRANSPORT
• Organism(s): Mus musculus
• Expression System: Escherichia coli


• Deposited: 2005-05-13 Released: 2005-10-26 
• Deposition Author(s): Siebold, C., Berrow, N., Walter, T.S., Harlos, K., Owens, R.J., Terman, J.R., Stuart, D.I., Kolodkin, A.L., Pasterkamp, R.J., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.222 
• R-Value Work: 0.180 

Literature

High-Resolution Structure of the Catalytic Region of Mical (Molecule Interacting with Casl), a Multidomain Flavoenzyme-Signaling Molecule.

Siebold, C., Berrow, N., Walter, T.S., Harlos, K., Owens, R.J., Stuart, D.I., Terman, J.R., Kolodkin, A.L., Pasterkamp, R.J., Jones, E.Y.

(2005) Proc.Natl.Acad.Sci.USA 102: 16836

• PubMed: 16275925 
• DOI: 10.1073/pnas.0504997102
• Primary Citation of Related Structures:  
  2C4C


• PubMed Abstract: 
  

Semaphorins are extracellular cell guidance cues that govern cytoskeletal dynamics during neuronal and vascular development. MICAL (molecule interacting with CasL) is a multidomain cytosolic protein with a putative flavoprotein monooxygenase (MO) region required for semaphorin-plexin repulsive axon guidance. Here, we report the 1.45-A resolution crystal structure of the FAD-containing MO domain of mouse MICAL-1 (residues 1-489). The topology most closely resembles that of the NADPH-dependent flavoenzyme p-hydroxybenzoate hydroxylase (PHBH). Comparison of structures before and after reaction with NADPH reveals that, as in PHBH, the flavin ring can switch between two discrete positions. In contrast with other MOs, this conformational switch is coupled with the opening of a channel to the active site, suggestive of a protein substrate. In support of this hypothesis, distinctive structural features highlight putative protein-binding sites in suitable proximity to the active site entrance. The unusual juxtaposition of this N-terminal MO (hydroxylase) activity with the characteristics of a multiprotein-binding scaffold exhibited by the C-terminal portion of the MICALs represents a unique combination of functionality to mediate signaling.

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Organizational Affiliation: 

Cancer Research UK Receptor Structure Research Group, Division of Structural Biology, University of Oxford, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NEDD9 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS	A, B	497	Mus musculus	Mutation(s): 0  Gene Names: Mical1 (Mical, Nical) EC: 1.14.13.225
Find proteins for Q8VDP3 (Mus musculus) Go to UniProtKB:  Q8VDP3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
FAD	A, B	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.222 
• R-Value Work: 0.180 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 76.588	α = 90.00
b = 89.548	β = 114.35
c = 83.458	γ = 90.00

Software Package:

Software Name	Purpose
SHELXD	phasing
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-13 
• Released Date: 2005-10-26 
• Deposition Author(s): Siebold, C., Berrow, N., Walter, T.S., Harlos, K., Owens, R.J., Terman, J.R., Stuart, D.I., Kolodkin, A.L., Pasterkamp, R.J., Jones, E.Y.

Revision History 

• Version 1.0: 2005-10-26
  Type: Initial release
• Version 1.1: 2011-05-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance