Database accession: MF7000657
Name: SbSOMT with pterostilbene and NAD+
PDB ID: 7was
Experimental method: X-ray (2.40 Å)
Assembly: Homodimer
Source organism: Sorghum bicolor
Primary publication of the structure:
Lui ACW, Pow KC, Lin N, Lam LPY, Liu G, Godwin ID, Fan Z, Khoo CJ, Tobimatsu Y, Wang L, Hao Q, Lo C
Regioselective stilbene O-methylations in Saccharinae grasses.
(2023) Nat Commun 14: 3462
PMID: 37308495
Abstract:
O-Methylated stilbenes are prominent nutraceuticals but rarely produced by crops. Here, the inherent ability of two Saccharinae grasses to produce regioselectively O-methylated stilbenes is reported. A stilbene O-methyltransferase, SbSOMT, is first shown to be indispensable for pathogen-inducible pterostilbene (3,5-bis-O-methylated) biosynthesis in sorghum (Sorghum bicolor). Phylogenetic analysis indicates the recruitment of genus-specific SOMTs from canonical caffeic acid O-methyltransferases (COMTs) after the divergence of Sorghum spp. from Saccharum spp. In recombinant enzyme assays, SbSOMT and COMTs regioselectively catalyze O-methylation of stilbene A-ring and B-ring respectively. Subsequently, SOMT-stilbene crystal structures are presented. Whilst SbSOMT shows global structural resemblance to SbCOMT, molecular characterizations illustrate two hydrophobic residues (Ile144/Phe337) crucial for substrate binding orientation leading to 3,5-bis-O-methylations in the A-ring. In contrast, the equivalent residues (Asn128/Asn323) in SbCOMT facilitate an opposite orientation that favors 3'-O-methylation in the B-ring. Consistently, a highly-conserved COMT is likely involved in isorhapontigenin (3'-O-methylated) formation in wounded wild sugarcane (Saccharum spontaneum). Altogether, our work reveals the potential of Saccharinae grasses as a source of O-methylated stilbenes, and rationalize the regioselectivity of SOMT activities for bioengineering of O-methylated stilbenes.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
nucleotide binding nucleotide binding
O-methyltransferase activity O-methyltransferase activity
protein dimerization activity protein dimerization activity
S-adenosylmethionine-dependent methyltransferase activity S-adenosylmethionine-dependent methyltransferase 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, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: O-methyltransferase domain-containing protein
Source organism: Sorghum bicolor
Length: 377 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGSYDSSSSSSNDSSARNEEDESCMFALKLLGGFAVPFTIKAVIELGVMDQLLTAERAMSAEELVAAAVAAQLPRPEVACTMVDRLLRFLASHSVVRCTTEVVVGTDDATTTTCCRRSYAASPVCKWFARNGVEDSVLPLGMMILNKTFLDSWQNITDAVLEGAAPFEKTYGMPMFEYLSTNGPLNTVFHEAMANHSMIITKKLLKFFRGFEGLDVLVDVGGGNGTTLQMIRGQYKNMRGINYDLPHVIAQAAPVEGVEHVGGSMFDNIPRGNAVLLKWILHDWDDKACIKILKNCYTALHVRGKVIVLEYVVPDEPEPTLAAQGAFELDLTMLVTFGSGKERTQREFSELAMEAGFSREFKATYIFANVWALEFTK
UniProtKB AC: A0A1B6PFV1 (positions: 15-377)
Coverage: 96%
Name: O-methyltransferase domain-containing protein
Source organism: Sorghum bicolor
Length: 377 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMGSYDSSSSSSNDSSARNEEDESCMFALKLLGGFAVPFTIKAVIELGVMDQLLTAERAMSAEELVAAAVAAQLPRPEVACTMVDRLLRFLASHSVVRCTTEVVVGTDDATTTTCCRRSYAASPVCKWFARNGVEDSVLPLGMMILNKTFLDSWQNITDAVLEGAAPFEKTYGMPMFEYLSTNGPLNTVFHEAMANHSMIITKKLLKFFRGFEGLDVLVDVGGGNGTTLQMIRGQYKNMRGINYDLPHVIAQAAPVEGVEHVGGSMFDNIPRGNAVLLKWILHDWDDKACIKILKNCYTALHVRGKVIVLEYVVPDEPEPTLAAQGAFELDLTMLVTFGSGKERTQREFSELAMEAGFSREFKATYIFANVWALEFTK
UniProtKB AC: A0A1B6PFV1 (positions: 15-377)
Coverage: 96%
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 B:
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)
Download this entry's JSON file (.json)
