1JEN

HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 A resolution reveals a novel fold.

Ekstrom, J.L.Mathews, I.I.Stanley, B.A.Pegg, A.E.Ealick, S.E.

(1999) Structure 7: 583-595

  • DOI: https://doi.org/10.1016/s0969-2126(99)80074-4
  • Primary Citation of Related Structures:  
    1JEN

  • PubMed Abstract: 

    S-Adenosylmethionine decarboxylase (AdoMetDC) is a critical regulatory enzyme of the polyamine synthetic pathway, and a well-studied drug target. The AdoMetDC decarboxylation reaction depends upon a pyruvoyl cofactor generated via an intramolecular proenzyme self-cleavage reaction. Both the proenzyme-processing and substrate-decarboxylation reactions are allosterically enhanced by putrescine. Structural elucidation of this enzyme is necessary to fully interpret the existing mutational and inhibitor-binding data, and to suggest further experimental studies. The structure of human AdoMetDC has been determined to 2.25 A resolution using multiwavelength anomalous diffraction (MAD) phasing methods based on 22 selenium-atom positions. The quaternary structure of the mature AdoMetDC is an (alpha beta)2 dimer, where alpha and beta represent the products of the proenzyme self-cleavage reaction. The architecture of each (alpha beta) monomer is a novel four-layer alpha/beta-sandwich fold, comprised of two antiparallel eight-stranded beta sheets flanked by several alpha and 3(10) helices. The structure and topology of AdoMetDC display internal symmetry, suggesting that this protein may be the product of an ancient gene duplication. The positions of conserved, functionally important residues suggest the location of the active site and a possible binding site for the effector molecule putrescine.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (BETA CHAIN))A [auth B],
C [auth D]
67Homo sapiensMutation(s): 0 
EC: 4.1.1.50
UniProt & NIH Common Fund Data Resources
Find proteins for P17707 (Homo sapiens)
Explore P17707 
Go to UniProtKB:  P17707
PHAROS:  P17707
GTEx:  ENSG00000123505 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17707
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (S-ADENOSYLMETHIONINE DECARBOXYLASE (ALPHA CHAIN))B [auth A],
D [auth C]
267Homo sapiensMutation(s): 0 
EC: 4.1.1.50
UniProt & NIH Common Fund Data Resources
Find proteins for P17707 (Homo sapiens)
Explore P17707 
Go to UniProtKB:  P17707
PHAROS:  P17707
GTEx:  ENSG00000123505 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17707
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.6α = 90
b = 55.8β = 109.6
c = 90.1γ = 90
Software Package:
Software NamePurpose
SnBphasing
SOLVEphasing
MLPHAREphasing
DMmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 2.0: 2023-11-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations