Structure of PDB 6vp5 Chain A

Receptor sequence

>6vp5A (length=335) Species: 319 (Pseudomonas savastanoi pv. phaseolicola)

MTNLQTFELPTEVTGCAADISLGRALIQAWQKDGIFQIKTDSEQDRKTQE
AMAASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCK
DLSVGDQRVKAGWPCHGPVPWPNNTYQKSMKTFMEELGLAGERLLKLTAL
GFELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTEYGLLVIAAQ
DDVGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVF
PGDILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPAN
ERIHYGEHFTNMFMRCYPDRITTQRINKENRLAHL

3D structure

• PDB: 6vp5 An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme.
• Chain: A
• Resolution: 1.97 Å

Enzymatic activity

• Enzyme Commision number: 1.13.12.19: 2-oxoglutarate dioxygenase (ethylene-forming).
  1.14.20.7: 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate- forming).

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	FE	A	H189 E191 H268	H189 E191 H268
BS02	AKG	A	R171 L173 F175 H189 E191 H268 V270 R277 A279	R171 L173 F175 H189 E191 H268 V270 R277 A279
BS03	ARG	A	E84 T86 R171 H189 E191 Y192 F314 R316 C317	E84 T86 R171 H189 E191 Y192 F313 R315 C316

Gene Ontology

Molecular Function

• GO:0016706 2-oxoglutarate-dependent dioxygenase activity
• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity
• GO:0102276 2-oxoglutarate oxygenase/decarboxylase (ethylene-forming) activity

Biological Process

• GO:0009693 ethylene biosynthetic process

External links

• PDB: RCSB:6vp5, PDBe:6vp5, PDBj:6vp5
• PDBsum: 6vp5
• PubMed: 33522811
• UniProt: P32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)