1M4N

CRYSTAL STRUCTURE OF APPLE ACC SYNTHASE IN COMPLEX WITH [2-(AMINO-OXY)ETHYL](5'-DEOXYADENOSIN-5'-YL)(METHYL)SULFONIUM

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 

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This is version 1.3 of the entry. See complete history. 


Literature

Structure of 1-aminocyclopropane-1-carboxylate synthase in complex with an amino-oxy analogue of the substrate: implications for substrate binding.

Capitani, G., Eliot, A.C., Gut, H., Khomutov, R.M., Kirsch, J.F., Grutter, M.G.

(2003) Biochim Biophys Acta Proteins Proteom 1647: 55-60

  • DOI: https://doi.org/10.1016/s1570-9639(03)00049-9
  • Primary Citation of Related Structures:  
    1M4N

  • PubMed Abstract: 

    The crystal structure of 1-aminocyclopropane-1-carboxylate (ACC) synthase in complex with the substrate analogue [2-(amino-oxy)ethyl](5'-deoxyadenosin-5'-yl)(methyl)sulfonium (AMA) was determined at 2.01-A resolution. The crystallographic results show that a covalent adduct (oxime) is formed between AMA (an amino-oxy analogue of the natural substrate S-adenosyl-L-methionine (SAM)) and the pyridoxal 5'-phosphate (PLP) cofactor of ACC synthase. The oxime formation is supported by spectroscopic data. The ACC synthase-AMA structure provides reliable and detailed information on the binding mode of the natural substrate of ACC synthase and complements previous structural and functional work on this enzyme.

    • Organizational Affiliation: 

    Biochemisches Institut der Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland. capitani@bioc.unizh.ch


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-aminocyclopropane-1-carboxylate synthase435Malus domesticaMutation(s): 0 
EC: 4.4.1.14
UniProt
Find proteins for P37821 (Malus domestica)
Explore P37821 
Go to UniProtKB:  P37821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37821
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AAD
Query on AAD
Download Ideal Coordinates CCD File 
C [auth A](2-AMINOOXY-ETHYL)-[5-(6-AMINO-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDRO-FURAN-2-YLMETHYL]-METHYL-SULFONIUM
C13 H21 N6 O4 S
RMAOLICYOBWFLA-OCVRIJAPSA-N
PLP
Query on PLP
Download Ideal Coordinates CCD File 
B [auth A]PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
MES
Query on MES
Download Ideal Coordinates CCD File 
D [auth A]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.199 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105α = 90
b = 61.33β = 123.48
c = 76.94γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description