Database accession: MF7000638
Name: Isoflavone o-methyltransferase
PDB ID: 1fp2
Experimental method: X-ray (1.40 Å)
Assembly: Homodimer
Source organism: Medicago sativa
Primary publication of the structure:
Zubieta C, He XZ, Dixon RA, Noel JP
Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases.
(2001) Nat. Struct. Biol. 8: 271-9
PMID: 11224575
Abstract:
Chalcone O-methyltransferase (ChOMT) and isoflavone O-methyltransferase (IOMT) are S-adenosyl-l-methionine (SAM) dependent plant natural product methyltransferases involved in secondary metabolism in Medicago sativa (alfalfa). Here we report the crystal structure of ChOMT in complex with the product S-adenosyl-l-homocysteine and the substrate isoliquiritigenin (4,2',4'-trihydroxychalcone) refined to 1.8 A as well as the crystal structure of IOMT in complex with the products S-adenosyl-l-homocysteine and isoformononetin (4'-hydroxy-7-methoxyisoflavone) refined to 1.4 A. These two OMTs constitute the first plant methyltransferases to be structurally characterized and reveal a novel oligomerization domain and the molecular determinants for substrate selection. As such, this work provides a structural basis for understanding the substrate specificity of the diverse family of plant OMTs and facilitates the engineering of novel activities in this extensive class of natural product biosynthetic enzymes.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
isoflavone 7-O-methyltransferase activity isoflavone 7-O-methyltransferase activity
protein dimerization activity protein dimerization activity
Biological process:
aromatic compound biosynthetic process obsolete aromatic compound biosynthetic process
methylation methylation
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Isoflavone-7-O-methyltransferase 8
Source organism: Medicago sativa
Length: 352 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITKEEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLKYILHNWTDKDCLRILKKCKEAVTNDGKRGKVTIIDMVIDKKKDENQVTQIKLLMDVNMACLNGKERNEEEWKKLFIEAGFQHYKISPLTGFLSLIEIYP
UniProtKB AC: O24529 (positions: 8-352)
Coverage: 98%
Name: Isoflavone-7-O-methyltransferase 8
Source organism: Medicago sativa
Length: 352 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMASSINGRKPSEIFKAQALLYKHIYAFIDSMSLKWAVEMNIPNIIQNHGKPISLSNLVSILQVPSSKIGNVRRLMRYLAHNGFFEIITKEEESYALTVASELLVRGSDLCLAPMVECVLDPTLSGSYHELKKWIYEEDLTLFGVTLGSGFWDFLDKNPEYNTSFNDAMASDSKLINLALRDCDFVFDGLESIVDVGGGTGTTAKIICETFPKLKCIVFDRPQVVENLSGSNNLTYVGGDMFTSIPNADAVLLKYILHNWTDKDCLRILKKCKEAVTNDGKRGKVTIIDMVIDKKKDENQVTQIKLLMDVNMACLNGKERNEEEWKKLFIEAGFQHYKISPLTGFLSLIEIYP
UniProtKB AC: O24529 (positions: 8-352)
Coverage: 98%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Dimeric O-methyltransferase
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
Coniferyl alcohol 9-O-methyltransferase has an intertwined dimeric structure with large relative interaction surface. The active site is formed by both monomers and thus dimerization is critical for activity. The N-terminal helices form the dimerization subdomain and at the same time form the rear wall of the active-site cavity in the neighbouring monomer (PMID:23633600). Other 9-O-methyltransferase structures show similar features and exhibit no monomeric form in solution (PMID:11224575).
Chain A:
N/A
Chain A-2:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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