3KYD

Human SUMO E1~SUMO1-AMP tetrahedral intermediate mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active site remodelling accompanies thioester bond formation in the SUMO E1.

Olsen, S.K.Capili, A.D.Lu, X.Tan, D.S.Lima, C.D.

(2010) Nature 463: 906-912

  • DOI: 10.1038/nature08765
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remain ...

    E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.


    Organizational Affiliation

    Structural Biology, Sloan-Kettering Institute, New York, New York 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SUMO-activating enzyme subunit 1
A
346Homo sapiensMutation(s): 0 
Gene Names: SAE1 (AOS1, SUA1, UBLE1A)
Find proteins for Q9UBE0 (Homo sapiens)
Go to Gene View: SAE1
Go to UniProtKB:  Q9UBE0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUMO-activating enzyme subunit 2
B
551Homo sapiensMutation(s): 0 
Gene Names: UBA2 (SAE2, UBLE1B)
EC: 2.3.2.-
Find proteins for Q9UBT2 (Homo sapiens)
Go to Gene View: UBA2
Go to UniProtKB:  Q9UBT2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 1
D
115Homo sapiensMutation(s): 1 
Gene Names: SUMO1 (SMT3C, SMT3H3, UBL1)
Find proteins for P63165 (Homo sapiens)
Go to Gene View: SUMO1
Go to UniProtKB:  P63165
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
VMX
Query on VMX

Download SDF File 
Download CCD File 
D
5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine
C13 H21 N7 O5 S
GCNSCCULRVBOML-QYVSTXNMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 101.717α = 90.00
b = 115.608β = 90.00
c = 90.837γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
ADSCdata collection
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-12-05 
  • Released Date: 2010-02-16 
  • Deposition Author(s): Lima, C.D.

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description