PDBsum entry 6rv0

Transferase

PDB id: 6rv0

Contents

Protein chain

384 a.a.

Ligands

PMP

Waters ×13

PDB id:

6rv0

Name:

Transferase

Title:

Human alanine:glyoxylate aminotransferase major allele (agt-ma); with pmp in the active site

Structure:

Serine--pyruvate aminotransferase. Chain: a. Synonym: spt,alanine--glyoxylate aminotransferase,agt. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: agxt, agt1, spat. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.70Å R-factor: 0.262 R-free: 0.325

Authors:

G.Giardina,F.Cutruzzola,B.Cellini,D.Mirco

Key ref:

M.Dindo et al. (2019). Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1. Biochem J, 476, 3751-3768. PubMed id: 31794008

Date:

30-May-19 Release date: 08-Apr-20

Protein chain

P21549  (SPYA_HUMAN) -  Alanine--glyoxylate aminotransferase from Homo sapiens

Seq: 392 a.a.

Struc: 384 a.a.

Enzyme reactions

• Enzyme class 1: E.C.2.6.1.44 - alanine--glyoxylate transaminase.
• Reaction: glyoxylate + L-alanine = glycine + pyruvate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PMP) matches with 88.24% similarity)

• Enzyme class 2: E.C.2.6.1.51 - serine--pyruvate transaminase.
• Reaction: L-serine + pyruvate = 3-hydroxypyruvate + L-alanine
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PMP) matches with 88.24% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Biochem J 476:3751-3768 (2019)

PubMed id: 31794008

Cycloserine enantiomers are reversible inhibitors of human alanine:glyoxylate aminotransferase: implications for Primary Hyperoxaluria type 1.

M.Dindo, S.Grottelli, G.Annunziato, G.Giardina, M.Pieroni, G.Pampalone, A.Faccini, F.Cutruzzolà, P.Laurino, G.Costantino, B.Cellini.

ABSTRACT

Peroxisomal alanine:glyoxylate aminotransferase (AGT) is responsible for glyoxylate detoxification in human liver and utilizes pyridoxal 5'-phosphate (PLP) as coenzyme. The deficit of AGT leads to Primary Hyperoxaluria Type I (PH1), a rare disease characterized by calcium oxalate stones deposition in the urinary tract as a consequence of glyoxylate accumulation. Most missense mutations cause AGT misfolding, as in the case of the G41R, which induces aggregation and proteolytic degradation. We have investigated the interaction of wild-type AGT and the pathogenic G41R variant with d-cycloserine (DCS, commercialized as Seromycin), a natural product used as a second-line treatment of multidrug-resistant tuberculosis, and its synthetic enantiomer l-cycloserine (LCS). In contrast with evidences previously reported on other PLP-enzymes, both ligands are AGT reversible inhibitors showing inhibition constants in the micromolar range. While LCS undergoes half-transamination generating a ketimine intermediate and behaves as a classical competitive inhibitor, DCS displays a time-dependent binding mainly generating an oxime intermediate. Using a mammalian cellular model, we found that DCS, but not LCS, is able to promote the correct folding of the G41R variant, as revealed by its increased specific activity and expression as a soluble protein. This effect also translates into an increased glyoxylate detoxification ability of cells expressing the variant upon treatment with DCS. Overall, our findings establish that DCS could play a role as pharmacological chaperone, thus suggesting a new line of intervention against PH1 based on a drug repositioning approach. To a widest extent, this strategy could be applied to other disease-causing mutations leading to AGT misfolding.