3KYC

Human SUMO E1 complex with a SUMO1-AMP mimic

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    3KYC, 3KYD

  • 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 remains unknown ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 1A346Homo sapiensMutation(s): 0 
Gene Names: AOS1, SAE1, SUA1, UBLE1A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBE0 (Homo sapiens)
Explore Q9UBE0 
Go to UniProtKB:  Q9UBE0
PHAROS:  Q9UBE0
Entity Groups  
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UniProt GroupQ9UBE0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-activating enzyme subunit 2B660Homo sapiensMutation(s): 1 
Gene Names: HRIHFB2115, SAE2, UBA2, UBLE1B
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBT2 (Homo sapiens)
Explore Q9UBT2 
Go to UniProtKB:  Q9UBT2
PHAROS:  Q9UBT2
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UniProt GroupQ9UBT2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Small ubiquitin-related modifier 1C [auth D]97Homo sapiensMutation(s): 1 
Gene Names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
UniProt & NIH Common Fund Data Resources
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
PHAROS:  P63165
Entity Groups  
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UniProt GroupP63165
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JZU
Query on JZU
Download Ideal Coordinates CCD File 
E [auth D]5'-deoxy-5'-(sulfamoylamino)adenosine
C10 H15 N7 O5 S
RCHUICYCIUKUIY-KQYNXXCUSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.174α = 90
b = 133.365β = 90
c = 159.656γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 


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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  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2021-10-13
    Changes: Database references, Derived calculations