6H78

E1 enzyme for ubiquitin like protein activation.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

An N-Terminal Extension to UBA5 Adenylation Domain Boosts UFM1 Activation: Isoform-Specific Differences in Ubiquitin-like Protein Activation.

Soudah, N.Padala, P.Hassouna, F.Kumar, M.Mashahreh, B.Lebedev, A.A.Isupov, M.N.Cohen-Kfir, E.Wiener, R.

(2019) J Mol Biol 431: 463-478

  • DOI: https://doi.org/10.1016/j.jmb.2018.10.007
  • Primary Citation of Related Structures:  
    6H77, 6H78

  • PubMed Abstract: 

    Modification of proteins by the ubiquitin-like protein, UFM1, requires activation of UFM1 by the E1-activating enzyme, UBA5. In humans, UBA5 possesses two isoforms, each comprising an adenylation domain, but only one containing an N-terminal extension. Currently, the role of the N-terminal extension in UFM1 activation is not clear. Here we provide structural and biochemical data on UBA5 N-terminal extension to understand its contribution to UFM1 activation. The crystal structures of the UBA5 long isoform bound to ATP with and without UFM1 show that the N-terminus not only is directly involved in ATP binding but also affects how the adenylation domain interacts with ATP. Surprisingly, in the presence of the N-terminus, UBA5 no longer retains the 1:2 ratio of ATP to UBA5, but rather this becomes a 1:1 ratio. Accordingly, the N-terminus significantly increases the affinity of ATP to UBA5. Finally, the N-terminus, although not directly involved in the E2 binding, stimulates transfer of UFM1 from UBA5 to the E2, UFC1.


  • Organizational Affiliation

    The Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like modifier-activating enzyme 5
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
300Homo sapiensMutation(s): 0 
Gene Names: UBA5UBE1DC1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ9 (Homo sapiens)
Explore Q9GZZ9 
Go to UniProtKB:  Q9GZZ9
GTEx:  ENSG00000081307 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9GZZ9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
ED [auth O]
FB [auth G]
FC [auth K]
GA [auth C]
LA [auth D]
ED [auth O],
FB [auth G],
FC [auth K],
GA [auth C],
LA [auth D],
LD [auth P],
MB [auth H],
MC [auth L],
Q [auth A],
RB [auth I],
SA [auth E],
TC [auth M],
VB [auth J],
X [auth B],
YA [auth F],
ZC [auth N]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AB [auth F]
BD [auth N]
GD [auth O]
HB [auth G]
HC [auth K]
AB [auth F],
BD [auth N],
GD [auth O],
HB [auth G],
HC [auth K],
IA [auth C],
NA [auth D],
ND [auth P],
OB [auth H],
OC [auth L],
S [auth A],
TB [auth I],
UA [auth E],
VC [auth M],
XB [auth J],
Z [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AC [auth J]
BA [auth B]
BC [auth J]
CA [auth B]
CB [auth F]
AC [auth J],
BA [auth B],
BC [auth J],
CA [auth B],
CB [auth F],
CC [auth J],
DA [auth B],
DB [auth F],
DC [auth J],
DD [auth N],
EA [auth B],
EB [auth F],
EC [auth J],
FA [auth B],
ID [auth O],
JB [auth G],
JC [auth K],
JD [auth O],
KA [auth C],
KB [auth G],
KC [auth K],
KD [auth O],
LB [auth G],
PA [auth D],
PD [auth P],
QA [auth D],
QB [auth H],
QC [auth L],
QD [auth P],
RA [auth D],
RC [auth L],
RD [auth P],
SC [auth L],
SD [auth P],
U [auth A],
V [auth A],
W [auth A],
WA [auth E],
XA [auth E],
XC [auth M],
YC [auth M],
ZB [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
LC [auth K]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth B]
AD [auth N]
BB [auth F]
CD [auth N]
FD [auth O]
AA [auth B],
AD [auth N],
BB [auth F],
CD [auth N],
FD [auth O],
GB [auth G],
GC [auth K],
HA [auth C],
HD [auth O],
IB [auth G],
IC [auth K],
JA [auth C],
MA [auth D],
MD [auth P],
NB [auth H],
NC [auth L],
OA [auth D],
OD [auth P],
PB [auth H],
PC [auth L],
R [auth A],
SB [auth I],
T [auth A],
TA [auth E],
UB [auth I],
UC [auth M],
VA [auth E],
WB [auth J],
WC [auth M],
Y [auth B],
YB [auth J],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.86α = 90
b = 151.933β = 93.07
c = 153.543γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description