3IHR

Crystal Structure of Uch37

• PDB DOI: https://doi.org/10.2210/pdb3IHR/pdb

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


• Deposited: 2009-07-30 Released: 2009-08-11 
• Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

Literature

Structural characterization of human Uch37.

Burgie, S.E., Bingman, C.A., Soni, A.B., Phillips Jr., G.N.

(2012) Proteins 80: 649-654

• PubMed: 21953935 
• DOI: https://doi.org/10.1002/prot.23147
• Primary Citation of Related Structures:  
  3IHR


• PubMed Abstract: 
  

  Uch37 is a de-ubiquitylating enzyme that is functionally linked with the 26S proteasome via Rpn13, and is essential for metazoan development. Here, we report the X-ray crystal structure of full-length human Uch37 at 2.95 Å resolution. Uch37's catalytic domain is similar to those of all UCH enzymes characterized to date. The C-terminal extension is elongated, predominantly helical and contains coiled coil interactions. Additionally, we provide an initial characterization of Uch37's oligomeric state and identify a systematic error in previous analyses of Uch37 activity. Taken together, these data provide a strong foundation for further analysis of Uch37's several functions.

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Organizational Affiliation: 

Department of Biochemistry, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison Wisconsin 53706-1544.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 38.02 kDa 
• Atom Count: 2,299 
• Modelled Residue Count: 282 
• Deposited Residue Count: 328 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase isozyme L5	A	328	Homo sapiens	Mutation(s): 1  Gene Names: AD-019, CGI-70, UCH37, UCHL5 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y5K5 (Homo sapiens) Explore Q9Y5K5  Go to UniProtKB:  Q9Y5K5
PHAROS:  Q9Y5K5 GTEx:  ENSG00000116750

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A], C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.242 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.092	α = 90
b = 98.736	β = 90
c = 154.061	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
DM	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-08-11 
Deposition Author(s): Burgie, E.S., Bingman, C.A., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2009-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-10-10
  Changes: Database references
• Version 1.3: 2013-01-09
  Changes: Database references
• Version 1.4: 2013-01-23
  Changes: Database references
• Version 1.5: 2013-06-19
  Changes: Database references
• Version 1.6: 2017-11-01
  Changes: Refinement description
• Version 1.7: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.8: 2023-07-26
  Changes: Database references
• Version 1.9: 2024-11-27
  Changes: Data collection, Structure summary