Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.71 kDa 
• Atom Count: 752 
• Residue Count: 99 
• Unique protein chains: 1

2L52

Solution structure of the small archaeal modifier protein 1 (SAMP1) from Methanosarcina acetivorans

• DOI: 10.2210/pdb2L52/pdb
• BMRB: 17263

• Classification: PROTEIN BINDING
• Organism(s): Methanosarcina acetivorans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-10-24 Released: 2011-02-09 
• Deposition Author(s): Damberger, F.F., Ranjan, N., Sutter, M., Allain, F.H.-T., Weber-Ban, E.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure and activation mechanism of ubiquitin-like small archaeal modifier proteins.

Ranjan, N., Damberger, F.F., Sutter, M., Allain, F.H., Weber-Ban, E.

(2011) J Mol Biol 405: 1040-1055

• PubMed: 21112336 
• DOI: 10.1016/j.jmb.2010.11.040
• Primary Citation of Related Structures:  
  2L52


• PubMed Abstract: 
  

In archaea, two ubiquitin-like small archaeal modifier protein (SAMPs) were recently shown to be conjugated to proteins in vivo. SAMPs display homology to bacterial MoaD sulfur transfer proteins and eukaryotic ubiquitin-like proteins, and they share with them the conserved C-terminal glycine-glycine motif. Here, we report the solution structure of SAMP1 from Methanosarcina acetivorans and the activation of SAMPs by an archaeal protein with homology to eukaryotic E1 enzymes. Our results show that SAMP1 possesses a β-grasp fold and that its hydrophobic and electrostatic surface features are similar to those of MoaD. M. acetivorans SAMP1 exhibits an extensive flexible surface loop between helix-2 and the third strand of the β-sheet, which contributes to an elongated surface groove that is not observed in bacterial ubiquitin homologues and many other SAMPs. We provide in vitro biochemical evidence that SAMPs are activated in an ATP-dependent manner by an E1-like enzyme that we have termed E1-like SAMP activator (ELSA). We show that activation occurs by formation of a mixed anhydride (adenylate) at the SAMP C-terminus and is detectable by SDS-PAGE and electrospray ionization mass spectrometry.

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, Schafmattstr. 20, ETH Zürich, CH-8093 Zürich, Switzerland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
METHANOSARCINA ACETIVORANS SAMP1 HOMOLOG	A	99	Methanosarcina acetivorans	Mutation(s): 0  Gene Names: moaD, MA_4086
Find proteins for Q8TIQ6 (Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)) Explore Q8TIQ6  Go to UniProtKB:  Q8TIQ6

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 120 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2L52 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-10-24 
• Released Date: 2011-02-09 
Deposition Author(s): Damberger, F.F., Ranjan, N., Sutter, M., Allain, F.H.-T., Weber-Ban, E.

Revision History 

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-05
  Changes: Data collection, Database references, Other