2Z6O | pdb_00002z6o

Crystal Structure of the Ufc1, Ufm1 conjugating enzyme 1

• PDB DOI: https://doi.org/10.2210/pdb2Z6O/pdb

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


• Deposited: 2007-08-06 Released: 2007-09-25 
• Deposition Author(s): Mizushima , T., Tatsumi, K., Ozaki, Y., Kawakami, T., Suzuki, A., Ogasahara, K., Komatsu, M., Kominami, E., Tanaka, K., Yamane, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Ufc1, the Ufm1-conjugating enzyme

Mizushima, T., Tatsumi, K., Ozaki, Y., Kawakami, T., Suzuki, A., Ogasahara, K., Komatsu, M., Kominami, E., Tanaka, K., Yamane, T.

(2007) Biochem Biophys Res Commun 362: 1079-1084

• PubMed: 17825256 
• DOI: https://doi.org/10.1016/j.bbrc.2007.08.129
• Primary Citation Related Structures: 
  2Z6O, 2Z6P


• PubMed Abstract: 
  

  Ubiquitin and ubiquitin-like protein-conjugating enzymes play central roles in posttranslational modification processes. The ubiquitin-fold modifier 1 (Ufm1), one of a variety of ubiquitin-like modifiers, is covalently attached to target proteins via Uba5 and Ufm1-conjugating enzyme 1 (Ufc1), which are analogous to the E1 and E2 ubiquitylation enzymes. As Ufm1-related proteins are conserved in metazoa and plants, the Ufm1 system likely plays important roles in various multicellular organisms. Herein, we report the X-ray structure of human Ufc1 determined at 1.6 A resolution. The Ufc1 structure comprises a canonical E2 domain and an additional N-terminal domain. The Uba5 binding site on Ufc1 was assigned by structural comparison of Ufc1 and Ubc12 and related mutational analyses. In addition, we show that the N-terminal unique domain of Ufc1 contributes to thermal stability.

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Organizational Affiliation: 
• Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya 464-8603, Japan.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 19.92 kDa 
• Atom Count: 1,492 
• Modeled Residue Count: 166 
• Deposited Residue Count: 172 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ufm1-conjugating enzyme 1	A	172	Homo sapiens	Mutation(s): 0  Gene Names: UFC1 EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3C8 (Homo sapiens) Explore Q9Y3C8  Go to UniProtKB:  Q9Y3C8
PHAROS:  Q9Y3C8 GTEx:  ENSG00000143222

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.221 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.37	α = 90
b = 47.601	β = 90
c = 82.34	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-25 
Deposition Author(s): Mizushima , T., Tatsumi, K., Ozaki, Y., Kawakami, T., Suzuki, A., Ogasahara, K., Komatsu, M., Kominami, E., Tanaka, K., Yamane, T.

Revision History  

• Version 1.0: 2007-09-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description