3IWB

T. maritima AdoMetDC in processed form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity.

Bale, S.Baba, K.McCloskey, D.E.Pegg, A.E.Ealick, S.E.

(2010) Acta Crystallogr.,Sect.D 66: 181-189

  • DOI: 10.1107/S090744490904877X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-bios ...

    The polyamines putrescine, spermidine and spermine are ubiquitous aliphatic cations and are essential for cellular growth and differentiation. S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical pyruvoyl-dependent enzyme in the polyamine-biosynthetic pathway. The crystal structures of AdoMetDC from humans and plants and of the AdoMetDC proenzyme from Thermotoga maritima have been obtained previously. Here, the crystal structures of activated T. maritima AdoMetDC (TmAdoMetDC) and of its complexes with S-adenosylmethionine methyl ester and 5'-deoxy-5'-dimethylthioadenosine are reported. The results demonstrate for the first time that TmAdoMetDC autoprocesses without the need for additional factors and that the enzyme contains two complete active sites, both of which use residues from both chains of the homodimer. The complexes provide insights into the substrate specificity and ligand binding of AdoMetDC in prokaryotes. The conservation of the ligand-binding mode and the active-site residues between human and T. maritima AdoMetDC provides insight into the evolution of AdoMetDC.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S-adenosylmethionine decarboxylase
B, D
62Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: speH
EC: 4.1.1.50
Find proteins for Q9WZC3 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZC3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S-adenosylmethionine decarboxylase
A, C
68Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)Mutation(s): 0 
Gene Names: speH
EC: 4.1.1.50
Find proteins for Q9WZC3 (Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099))
Go to UniProtKB:  Q9WZC3
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PYR
Query on PYR
A, C
NON-POLYMERC3 H4 O3

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.233 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 104.712α = 90.00
b = 104.712β = 90.00
c = 69.839γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CrystalCleardata collection
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
HKL-2000data reduction
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Advisory, Refinement description