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 
  • R-Value Observed: 0.230 

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
  • Structures With Same Primary Citation

  • 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 1A346Homo sapiensMutation(s): 0 
Gene Names: AOS1SAE1SUA1UBLE1A
Find proteins for Q9UBE0 (Homo sapiens)
Explore Q9UBE0 
Go to UniProtKB:  Q9UBE0
NIH Common Fund Data Resources
PHAROS  Q9UBE0
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SUMO-activating enzyme subunit 2B551Homo sapiensMutation(s): 1 
Gene Names: HRIHFB2115SAE2UBA2UBLE1B
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
NIH Common Fund Data Resources
PHAROS  Q9UBT2
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 1D115Homo sapiensMutation(s): 1 
Gene Names: OK/SW-cl.43SMT3CSMT3H3SUMO1UBL1
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VMX
Query on VMX

Download CCD File 
D
5'-{[(3-aminopropyl)sulfonyl]amino}-5'-deoxyadenosine
C13 H21 N7 O5 S
GCNSCCULRVBOML-QYVSTXNMSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-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 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.717α = 90
b = 115.608β = 90
c = 90.837γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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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
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description