1M4N | pdb_00001m4n

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

• PDB DOI: https://doi.org/10.2210/pdb1M4N/pdb

• Classification: LYASE
• Organism(s): Malus domestica
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-07-03 Released: 2003-04-22 
• Deposition Author(s): Capitani, G., Eliot, A.C., Gut, H., Khomutov, R.M., Kirsch, J.F., Grutter, M.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 
  0.232 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.194 (DCC) 

Starting Model: experimental

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

• PubMed: 12686108 
• DOI: https://doi.org/10.1016/s1570-9639(03)00049-9
• Primary Citation 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. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 49.89 kDa 
• Atom Count: 3,681 
• Modeled Residue Count: 421 
• Deposited Residue Count: 435 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-aminocyclopropane-1-carboxylate synthase	A	435	Malus domestica	Mutation(s): 0  EC: 4.4.1.14 (PDB Primary Data), 1.4 (UniProt)
UniProt
Find proteins for P37821 (Malus domestica) Explore P37821  Go to UniProtKB:  P37821

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AAD	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	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MES	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 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.194 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105	α = 90
b = 61.33	β = 123.48
c = 76.94	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Capitani, G., Eliot, A.C., Gut, H., Khomutov, R.M., Kirsch, J.F., Grutter, M.G.

Revision History  

• 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