1R5X

JAMM: A Metalloprotease-like Zinc Site in the Proteasome and Signalosome

• PDB DOI: https://doi.org/10.2210/pdb1R5X/pdb

• Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
• Organism(s): Archaeoglobus fulgidus DSM 4304
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-13 Released: 2003-11-25 
• Deposition Author(s): Ambroggio, X.I., Rees, D.C., Deshaies, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.263 (Depositor) 

Literature

JAMM: a metalloprotease-like zinc site in the proteasome and signalosome.

Ambroggio, X.I., Rees, D.C., Deshaies, R.J.

(2004) PLoS Biol 2: E2-E2

• PubMed: 14737182 
• DOI: https://doi.org/10.1371/journal.pbio.0020002
• Primary Citation of Related Structures:  
  1R5X


• PubMed Abstract: 
  

  The JAMM (JAB1/MPN/Mov34 metalloenzyme) motif in Rpn11 and Csn5 underlies isopeptidase activities intrinsic to the proteasome and signalosome, respectively. We show here that the archaebacterial protein AfJAMM possesses the key features of a zinc metalloprotease, yet with a distinct fold. The histidine and aspartic acid of the conserved EX(n)HS/THX(7)SXXD motif coordinate a zinc, whereas the glutamic acid hydrogen-bonds an aqua ligand. By analogy to the active site of thermolysin, we predict that the glutamic acid serves as an acid-base catalyst and the second serine stabilizes a tetrahedral intermediate. Mutagenesis of Csn5 confirms these residues are required for Nedd8 isopeptidase activity. The active site-like architecture specified by the JAMM motif motivates structure-based approaches to the study of JAMM domain proteins and the development of therapeutic proteasome and signalosome inhibitors.

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Organizational Affiliation: 

Division of Biology, California Institute of Technology, Pasadena, California, USA.

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: 30.22 kDa 
• Atom Count: 1,741 
• Modelled Residue Count: 206 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AfJAMM	A, B	133	Archaeoglobus fulgidus DSM 4304	Mutation(s): 0  Gene Names: AF2198
UniProt
Find proteins for O28085 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28085  Go to UniProtKB:  O28085

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.308 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.263 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.161	α = 90
b = 76.161	β = 90
c = 92.124	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-11-25 
Deposition Author(s): Ambroggio, X.I., Rees, D.C., Deshaies, R.J.

Revision History  

• Version 1.0: 2003-11-25
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations