4PF1

Crystal structure of aminopeptidase from marine sediment archaeon Thaumarchaeota archaeon


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

New aminopeptidase from "microbial dark matter" archaeon.

Michalska, K.Steen, A.D.Chhor, G.Endres, M.Webber, A.T.Bird, J.Lloyd, K.G.Joachimiak, A.

(2015) FASEB J. 29: 4071-4079

  • DOI: 10.1096/fj.15-272906

  • PubMed Abstract: 
  • Marine sediments host a large population of diverse, heterotrophic, uncultured microorganisms with unknown physiologies that control carbon flow through organic matter decomposition. Recently, single-cell genomics uncovered new key players in these p ...

    Marine sediments host a large population of diverse, heterotrophic, uncultured microorganisms with unknown physiologies that control carbon flow through organic matter decomposition. Recently, single-cell genomics uncovered new key players in these processes, such as the miscellaneous crenarchaeotal group. These widespread archaea encode putative intra- and extracellular proteases for the degradation of detrital proteins present in sediments. Here, we show that one of these enzymes is a self-compartmentalizing tetrameric aminopeptidase with a preference for cysteine and hydrophobic residues at the N terminus of the hydrolyzed peptide. The ability to perform detailed characterizations of enzymes from native subsurface microorganisms, without requiring that those organisms first be grown in pure culture, holds great promise for understanding key carbon transformations in the environment as well as identifying new enzymes for biomedical and biotechnological applications.


    Organizational Affiliation

    *Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA; Department of Microbiology and Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA; and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,*Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, Illinois, USA; Department of Microbiology and Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee, USA; and Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA andrzejj@anl.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidase S15/CocE/NonD
A, B, C, D
626Thaumarchaeota archaeon SCGC AB-539-E09Mutation(s): 0 
Find proteins for M7TVE7 (Thaumarchaeota archaeon SCGC AB-539-E09)
Go to UniProtKB:  M7TVE7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B, D
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 118.434α = 90.00
b = 108.144β = 95.08
c = 120.384γ = 90.00
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585

Revision History 

  • Version 1.0: 2014-06-11
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2017-11-08
    Type: Database references