Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 13.55 kDa 
• Atom Count: 954 
• Residue Count: 120 
• Unique protein chains: 2

2KSP

Mechanism for the selective interaction of C-terminal EH-domain proteins with specific NPF-containing partners

• DOI: 10.2210/pdb2KSP/pdb
• BMRB: 16671

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-01-11 Released: 2010-01-26 
• Deposition Author(s): Kieken, F., Sharma, M., Jovic, M., Giridharan, S.S., Naslavsky, N., Caplan, S., Sorgen, P.L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Mechanism for the selective interaction of C-terminal Eps15 homology domain proteins with specific Asn-Pro-Phe-containing partners.

Kieken, F., Sharma, M., Jovic, M., Giridharan, S.S., Naslavsky, N., Caplan, S., Sorgen, P.L.

(2010) J Biol Chem 285: 8687-8694

• PubMed: 20106972 
• DOI: 10.1074/jbc.M109.045666
• Primary Citation of Related Structures:  
  2KSP


• PubMed Abstract: 
  

Epidermal growth factor receptor tyrosine kinase substrate 15 (Eps15) homology (EH)-domain proteins can be divided into two classes: those with an N-terminal EH-domain(s), and the C-terminal Eps15 homology domain-containing proteins (EHDs). Whereas many N-terminal EH-domain proteins regulate internalization events, the best characterized C-terminal EHD, EHD1, regulates endocytic recycling. Because EH-domains interact with the tripeptide Asn-Pro-Phe (NPF), it is of critical importance to elucidate the molecular mechanisms that allow EHD1 and its paralogs to interact selectively with a subset of the hundreds of NPF-containing proteins expressed in mammalian cells. Here, we capitalize on our findings that C-terminal EH-domains possess highly positively charged interaction surfaces and that many NPF-containing proteins that interact with C-terminal (but not N-terminal) EH-domains are followed by acidic residues. Using the recently identified EHD1 interaction partner molecule interacting with CasL (MICAL)-Like 1 (MICAL-L1) as a model, we have demonstrated that only the first of its two NPF motifs is required for EHD1 binding. Because only this first NPF is followed by acidic residues, we have utilized glutathione S-transferase pulldowns, two-hybrid analysis, and NMR to demonstrate that the flanking acidic residues "fine tune" the binding affinity to EHD1. Indeed, our NMR solution structure of the EHD1 EH-domain in complex with the MICAL-L1 NPFEEEEED peptide indicates that the first two flanking Glu residues lie in a position favorable to form salt bridges with Lys residues within the EH-domain. Our data provide a novel explanation for the selective interaction of C-terminal EH-domains with specific NPF-containing proteins and allow for the prediction of new interaction partners with C-terminal EHDs.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology and Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198-5870, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EH domain-containing protein 1	A	105	Homo sapiens	Mutation(s): 0  Gene Names: EHD1, PAST, PAST1, CDABP0131
Find proteins for Q9H4M9 (Homo sapiens) Explore Q9H4M9  Go to UniProtKB:  Q9H4M9
NIH Common Fund Data Resources
PHAROS  Q9H4M9 GTEx  ENSG00000110047

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MICAL L1 like peptide	B	15	N/A	Mutation(s): 0
Find proteins for Q8N3F8 (Homo sapiens) Explore Q8N3F8  Go to UniProtKB:  Q8N3F8
NIH Common Fund Data Resources
PHAROS  Q8N3F8 GTEx  ENSG00000100139

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 30 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2KSP Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-01-11 
• Released Date: 2010-01-26 
Deposition Author(s): Kieken, F., Sharma, M., Jovic, M., Giridharan, S.S., Naslavsky, N., Caplan, S., Sorgen, P.L.

Revision History 

• Version 1.0: 2010-01-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Database references, Derived calculations, Other