Structure of PDB 6vst Chain I

Receptor sequence

>6vstI (length=317) Species: 3880 (Medicago truncatula)

PALLEKAQNRVIDAALTFIRERAKFKGELMRSLGGVAATSSLLGVPLGHH
SSFHEGSAFAPPRIREAIWCDSTNSTTEEGKNLRDPRVITNVGDVPIEEI
RDCGVDDKRLANVISESVKLVMDEDPLRPLVLGGDHSISFPVVRAVSEKL
GGAVDILHFDAHPDLYHDFEGNYYSHASPFARIMEGGYARRLVQVGIRSI
TNDVREQVKKYGVETHEMRTLSRDRPILENLKLGEGVKGVYVSIDVDSLD
PSIAPGVSHHEPGGLLFRDILNILQNLQGDIVGGDVVEYNPQRDTYDGIT
ALVAAKLVRELAAKMSK

3D structure

• PDB: 6vst The Neighboring Subunit Is Engaged to Stabilize the Substrate in the Active Site of Plant Arginases.
• Chain: I
• Resolution: 2.12 Å

Enzymatic activity

• Enzyme Commision number: 3.5.3.1: arginase.
  3.5.3.11: agmatinase.

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	ORN	I	S93 N95	S72 N74
BS02	MN	I	D181 H183 D266 D268	D160 H162 D245 D247
BS03	MN	I	H157 D181 D185 D266	H136 D160 D164 D245

Gene Ontology

Molecular Function

• GO:0004053 arginase activity
• GO:0008783 agmatinase activity
• GO:0016787 hydrolase activity
• GO:0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines
• GO:0046872 metal ion binding

Biological Process

• GO:0000050 urea cycle
• GO:0006525 arginine metabolic process
• GO:0009446 putrescine biosynthetic process
• GO:0019547 arginine catabolic process to ornithine
• GO:0033388 putrescine biosynthetic process from arginine
• GO:0033389 putrescine biosynthetic process from arginine, using agmatinase
• GO:0034214 protein hexamerization

Cellular Component

• GO:0005739 mitochondrion

External links

• PDB: RCSB:6vst, PDBe:6vst, PDBj:6vst
• PDBsum: 6vst
• PubMed: 32754173
• UniProt: G7JFU5|ARGI_MEDTR Arginase, mitochondrial (Gene Name=ARGAH)