1FPR | pdb_00001fpr

CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN THE CATALYTIC DOMAIN OF SHP-1 AND AN IN VITRO PEPTIDE SUBSTRATE PY469 DERIVED FROM SHPS-1.

• PDB DOI: https://doi.org/10.2210/pdb1FPR/pdb

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


• Deposited: 2000-08-31 Released: 2001-03-07 
• Deposition Author(s): Yang, J., Cheng, Z., Niu, Z., Zhao, Z.J., Zhou, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.303 (Depositor) 
• R-Value Work: 
  0.194 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Structural basis for substrate specificity of protein-tyrosine phosphatase SHP-1.

Yang, J., Cheng, Z., Niu, T., Liang, X., Zhao, Z.J., Zhou, G.W.

(2000) J Biological Chem 275: 4066-4071

• PubMed: 10660565 
• DOI: https://doi.org/10.1074/jbc.275.6.4066
• Primary Citation Related Structures: 
  1FPR


• PubMed Abstract: 
  

  The substrate specificity of the catalytic domain of SHP-1, an important regulator in the proliferation and development of hematopoietic cells, is critical for understanding the physiological functions of SHP-1. Here we report the crystal structures of the catalytic domain of SHP-1 complexed with two peptide substrates derived from SIRPalpha, a member of the signal-regulatory proteins. We show that the variable beta5-loop-beta6 motif confers SHP-1 substrate specificity at the P-4 and further N-terminal subpockets. We also observe a novel residue shift at P-2, the highly conserved subpocket in protein- tyrosine phosphatases. Our observations provide new insight into the substrate specificity of SHP-1.

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Organizational Affiliation: 
• Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 33.79 kDa 
• Atom Count: 2,374 
• Modeled Residue Count: 294 
• Deposited Residue Count: 294 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN-TYROSINE PHOSPHATASE 1C	A	284	Homo sapiens	Mutation(s): 1  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29350 (Homo sapiens) Explore P29350  Go to UniProtKB:  P29350
PHAROS:  P29350 GTEx:  ENSG00000111679

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDE PY469	B	10	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	B	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.303 (Depositor) 
• R-Value Work:  0.194 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.58	α = 90
b = 45.21	β = 90
c = 56.27	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALEPACK	data scaling
AMoRE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-03-07 
Deposition Author(s): Yang, J., Cheng, Z., Niu, Z., Zhao, Z.J., Zhou, G.W.

Revision History  

• Version 1.0: 2001-03-07
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-10-16
  Changes: Data collection, Structure summary