Structure of PDB 5vka Chain A

Receptor sequence

>5vkaA (length=348) Species: 319 (Pseudomonas savastanoi pv. phaseolicola)

NLQTFELPTEVTGCAADISLGRALIQAWQKDGIFQIKTDSEQDRKTQEAM
AASKQFCKEPLTFKSSCVSDLTYSGYVASGEEVTAGKPDFPEIFTVCKDL
SVGDQRVKAGWPCHGPVPWPNNTYQKSMKTFMEELGLAGERLLKLTALGF
ELPINTFTDLTRDGWHHMRVLRFPPQTSTLSRGIGAHTDYGLLVIAAQDD
VGGLYIRPPVEGEKRNRNWLPGESSAGMFEHDEPWTFVTPTPGVWTVFPG
DILQFMTGGQLLSTPHKVKLNTRERFACAYFHEPNFEASAYPLFEPSANE
RIHYGEHFTNMFMRCYPDRITTQRINKENRLAHLEDLKKYSDTRATGS

3D structure

• PDB: 5vka Structures and Mechanisms of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme: Substrate Binding Creates a Twist.
• Chain: A
• Resolution: 1.169 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	MN	A	H189 D191 H268	H187 D189 H266
BS02	AKG	A	R171 L173 F175 H189 D191 H268 V270 R277 A279	R169 L171 F173 H187 D189 H266 V268 R275 A277
BS03	HAR	A	E84 T86 R171 H189 D191 Y192 F314 R316 C317	E82 T84 R169 H187 D189 Y190 F312 R314 C315

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:5vka, PDBe:5vka, PDBj:5vka
• PDBsum: 5vka
• PubMed: 28780854
• UniProt: P32021|EFE_PSESH 2-oxoglutarate-dependent ethylene/succinate-forming enzyme (Gene Name=efe)