1I1I | pdb_00001i1i

NEUROLYSIN (ENDOPEPTIDASE 24.16) CRYSTAL STRUCTURE

• PDB DOI: https://doi.org/10.2210/pdb1I1I/pdb

• Classification: HYDROLASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-02-01 Released: 2001-02-28 
• Deposition Author(s): Brown, C.K., Madauss, K., Lian, W., Tolbert, W.D., Beck, M.R., Rodgers, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.224 (DCC) 

Literature

Structure of neurolysin reveals a deep channel that limits substrate access.

Brown, C.K., Madauss, K., Lian, W., Beck, M.R., Tolbert, W.D., Rodgers, D.W.

(2001) Proc Natl Acad Sci U S A 98: 3127-3132

• PubMed: 11248043 
• DOI: https://doi.org/10.1073/pnas.051633198
• Primary Citation Related Structures: 
  1I1I


• PubMed Abstract: 
  

  The zinc metallopeptidase neurolysin is shown by x-ray crystallography to have large structural elements erected over the active site region that allow substrate access only through a deep narrow channel. This architecture accounts for specialization of this neuropeptidase to small bioactive peptide substrates without bulky secondary and tertiary structures. In addition, modeling studies indicate that the length of a substrate N-terminal to the site of hydrolysis is restricted to approximately 10 residues by the limited size of the active site cavity. Some structural elements of neurolysin, including a five-stranded beta-sheet and the two active site helices, are conserved with other metallopeptidases. The connecting loop regions of these elements, however, are much extended in neurolysin, and they, together with other open coil elements, line the active site cavity. These potentially flexible elements may account for the ability of the enzyme to cleave a variety of sequences.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 78.01 kDa 
• Atom Count: 5,522 
• Modeled Residue Count: 665 
• Deposited Residue Count: 681 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NEUROLYSIN	A [auth P]	681	Rattus norvegicus	Mutation(s): 0  EC: 3.4.24.16
UniProt
Find proteins for P42676 (Rattus norvegicus) Explore P42676  Go to UniProtKB:  P42676

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth P], C [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.268 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.224 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 157.6	α = 90
b = 87.7	β = 90
c = 58.3	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-02-28 
Deposition Author(s): Brown, C.K., Madauss, K., Lian, W., Tolbert, W.D., Beck, M.R., Rodgers, D.W.

Revision History  

• Version 1.0: 2001-02-28
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations