1JWA

Structure of the ATP-bound MoeB-MoaD Protein Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex.

Lake, M.W.Wuebbens, M.M.Rajagopalan, K.V.Schindelin, H.

(2001) Nature 414: 325-329

  • DOI: https://doi.org/10.1038/35104586
  • Primary Citation of Related Structures:  
    1JW9, 1JWA, 1JWB

  • PubMed Abstract: 

    The activation of ubiquitin and related protein modifiers is catalysed by members of the E1 enzyme family that use ATP for the covalent self-attachment of the modifiers to a conserved cysteine. The Escherichia coli proteins MoeB and MoaD are involved in molybdenum cofactor (Moco) biosynthesis, an evolutionarily conserved pathway. The MoeB- and E1-catalysed reactions are mechanistically similar, and despite a lack of sequence similarity, MoaD and ubiquitin display the same fold including a conserved carboxy-terminal Gly-Gly motif. Similar to the E1 enzymes, MoeB activates the C terminus of MoaD to form an acyl-adenylate. Subsequently, a sulphurtransferase converts the MoaD acyl-adenylate to a thiocarboxylate that acts as the sulphur donor during Moco biosynthesis. These findings suggest that ubiquitin and E1 are derived from two ancestral genes closely related to moaD and moeB. Here we present the crystal structures of the MoeB-MoaD complex in its apo, ATP-bound, and MoaD-adenylate forms, and highlight the functional similarities between the MoeB- and E1-substrate complexes. These structures provide a molecular framework for understanding the activation of ubiquitin, Rub, SUMO and the sulphur incorporation step during Moco and thiamine biosynthesis.


  • Organizational Affiliation

    Department of Biochemistry and Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, New York 11794-5115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEINA [auth B]249Escherichia coliMutation(s): 0 
Gene Names: MoeB
UniProt
Find proteins for P12282 (Escherichia coli (strain K12))
Explore P12282 
Go to UniProtKB:  P12282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12282
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1B [auth D]81Escherichia coliMutation(s): 0 
Gene Names: MoaD
UniProt
Find proteins for P30748 (Escherichia coli (strain K12))
Explore P30748 
Go to UniProtKB:  P30748
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30748
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
C [auth B]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.206 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.723α = 90
b = 78.723β = 90
c = 103.184γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-11-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations