2JEV

Crystal structure of human spermine,spermidine acetyltransferase in complex with a bisubstrate analog (N1-acetylspermine-S-CoA).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

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This is version 1.3 of the entry. See complete history


Literature

Mechanistic and Structural Analysis of Human Spermidine/Spermine N(1)-Acetyltransferase.

Hegde, S.S.Chandler, J.Vetting, M.W.Yu, M.Blanchard, J.S.

(2007) Biochemistry 46: 7187

  • DOI: 10.1021/bi700256z
  • Primary Citation of Related Structures:  
    2JEV

  • PubMed Abstract: 
  • The N1-acetylation of spermidine and spermine by spermidine/spermine acetyltransferase (SSAT) is a crucial step in the regulation of the cellular polyamine levels in eukaryotic cells. Altered polyamine levels are associated with a variety of cancers as well as other diseases, and key enzymes in the polyamine pathway, including SSAT, are being explored as potential therapeutic drug targets ...

    The N1-acetylation of spermidine and spermine by spermidine/spermine acetyltransferase (SSAT) is a crucial step in the regulation of the cellular polyamine levels in eukaryotic cells. Altered polyamine levels are associated with a variety of cancers as well as other diseases, and key enzymes in the polyamine pathway, including SSAT, are being explored as potential therapeutic drug targets. We have expressed and purified human SSAT in Escherichia coli and characterized its kinetic and chemical mechanism. Initial velocity and inhibition studies support a random sequential mechanism for the enzyme. The bisubstrate analogue, N1-spermine-acetyl-coenzyme A, exhibited linear, competitive inhibition against both substrates with a true Ki of 6 nM. The pH-activity profile was bell-shaped, depending on the ionization state of two groups exhibiting apparent pKa values of 7.27 and 8.87. The three-dimensional crystal structure of SSAT with bound bisubstrate inhibitor was determined at 2.3 A resolution. The structure of the SSAT-spermine-acetyl-coenzyme A complex suggested that Tyr140 acts as general acid and Glu92, through one or more water molecules, acts as the general base during catalysis. On the basis of kinetic properties, pH dependence, and structural information, we propose an acid/base-assisted reaction catalyzed by SSAT, involving a ternary complex.


    Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIAMINE ACETYLTRANSFERASE 1A, B174Homo sapiensMutation(s): 0 
Gene Names: SAT1SAT
EC: 2.3.1.57
UniProt & NIH Common Fund Data Resources
Find proteins for P21673 (Homo sapiens)
Explore P21673 
Go to UniProtKB:  P21673
PHAROS:  P21673
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21673
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NHQ
Query on NHQ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(3R)-27-AMINO-3-HYDROXY-2,2-DIMETHYL-4,8,14-TRIOXO-12-THIA-5,9,15,19,24-PENTAAZAHEPTACOS-1-YL [(2S,3R,4S,5S)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE
C33 H62 N11 O17 P3 S
BNNJEDLSMFSIRT-GMHMEAMDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
NHQ Binding MOAD:  2JEV Ki: 6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.729α = 90
b = 46.729β = 90
c = 191.792γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other