5IRI | pdb_00005iri

Structure of the mouse SAD-B AIS-KA1 fragment

• PDB DOI: https://doi.org/10.2210/pdb5IRI/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-03-13 Released: 2016-06-15 
• Deposition Author(s): Ma, H., Wu, J.X., Wang, J., Wu, J.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structure and inhibition analysis of the mouse SAD-B C-terminal fragment

Ma, H., Wu, J.X., Wang, J., Wang, Z.X., Wu, J.W.

(2016) Biosci Biotechnol Biochem 

• PubMed: 27251228 
• DOI: https://doi.org/10.1080/09168451.2016.1191331
• Primary Citation Related Structures: 
  5IRI


• PubMed Abstract: 
  

  The SAD (synapses of amphids defective) kinases, including SAD-A and SAD-B, play important roles in the regulation of neuronal development, cell cycle, and energy metabolism. Our recent study of mouse SAD-A identified a unique autoinhibitory sequence (AIS), which binds at the junction of the kinase domain (KD) and the ubiquitin-associated (UBA) domain and exerts autoregulation in cooperation with UBA. Here, we report the crystal structure of the mouse SAD-B C-terminal fragment including the AIS and the kinase-associated domain 1 (KA1) at 2.8 Å resolution. The KA1 domain is structurally conserved, while the isolated AIS sequence is highly flexible and solvent-accessible. Our biochemical studies indicated that the SAD-B AIS exerts the same autoinhibitory role as that in SAD-A. We believe that the flexible isolated AIS sequence is readily available for interaction with KD-UBA and thus inhibits SAD-B activity.

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Organizational Affiliation: 
• a MOE Key Laboratory of Protein Sciences and Tsinghua-Peking Center for Life Sciences , School of Life Sciences, Tsinghua University , Beijing , China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.7 kDa 
• Atom Count: 1,643 
• Modeled Residue Count: 210 
• Deposited Residue Count: 274 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase BRSK1	A, B	137	Mus musculus	Mutation(s): 0  Gene Names: Brsk1, Gm1100, Sadb EC: 2.7.11.26 (PDB Primary Data), 2.7.11.1 (UniProt)
UniProt
Find proteins for Q5RJI5 (Mus musculus) Explore Q5RJI5  Go to UniProtKB:  Q5RJI5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.265 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.839	α = 90
b = 86.839	β = 90
c = 91.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-06-15 
Deposition Author(s): Ma, H., Wu, J.X., Wang, J., Wu, J.W.

Revision History  

• Version 1.0: 2016-06-15
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description