4AMH | pdb_00004amh

Influence of circular permutation on the folding pathway of a PDZ domain

• PDB DOI: https://doi.org/10.2210/pdb4AMH/pdb

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


• Deposited: 2012-03-10 Released: 2012-12-05 
• Deposition Author(s): Hultqvist, G., Punekar, A.S., Chi, C.N., Selmer, M., Gianni, S., Jemth, P.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.268 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Tolerance of Protein Folding to a Circular Permutation in a Pdz Domain

Hultqvist, G., Punekar, A.S., Morrone, A., Chi, C.N., Engstrom, A., Selmer, M., Gianni, S., Jemth, P.

(2012) PLoS One 7: 50055

• PubMed: 23185531 
• DOI: https://doi.org/10.1371/journal.pone.0050055
• Primary Citation Related Structures: 
  4AMH


• PubMed Abstract: 
  

  Circular permutation is a common molecular mechanism for evolution of proteins. However, such re-arrangement of secondary structure connectivity may interfere with the folding mechanism causing accumulation of folding intermediates, which in turn can lead to misfolding. We solved the crystal structure and investigated the folding pathway of a circularly permuted variant of a PDZ domain, SAP97 PDZ2. Our data illustrate how well circular permutation may work as a mechanism for molecular evolution. The circular permutant retains the overall structure and function of the native protein domain. Further, unlike most examples in the literature, this circular permutant displays a folding mechanism that is virtually identical to that of the wild type. This observation contrasts with previous data on the circularly permuted PDZ2 domain from PTP-BL, for which the folding pathway was remarkably affected by the same mutation in sequence connectivity. The different effects of this circular permutation in two homologous proteins show the strong influence of sequence as compared to topology. Circular permutation, when peripheral to the major folding nucleus, may have little effect on folding pathways and could explain why, despite the dramatic change in primary structure, it is frequently tolerated by different protein folds.

---

Organizational Affiliation: 
• Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.96 kDa 
• Atom Count: 1,453 
• Modeled Residue Count: 186 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DISKS LARGE HOMOLOG 1	A, B	106	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q12959 (Homo sapiens) Explore Q12959  Go to UniProtKB:  Q12959
PHAROS:  Q12959 GTEx:  ENSG00000075711

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.268 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.9	α = 90
b = 43.6	β = 103.7
c = 51.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Hultqvist, G., Punekar, A.S., Chi, C.N., Selmer, M., Gianni, S., Jemth, P.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description