PDBsum entry 1ekf

Transferase

PDB id: 1ekf

Contents

Protein chain

365 a.a. *

Ligands

PLP ×2

Waters ×273

* Residue conservation analysis

PDB id:

1ekf

Name:

Transferase

Title:

Crystallographic structure of human branched chain amino acid aminotransferase (mitochondrial) complexed with pyridoxal-5'- phosphate at 1.95 angstroms (orthorhombic form)

Structure:

Branched chain amino acid aminotransferase (mitochondrial). Chain: a, b. Synonym: bcat(m). Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.222 R-free: 0.260

Authors:

N.H.Yennawar,J.H.Dunbar,M.Conway,S.M.Hutson,G.K.Farber

Key ref:

N.Yennawar et al. (2001). The structure of human mitochondrial branched-chain aminotransferase. Acta Crystallogr D Biol Crystallogr, 57, 506-515. PubMed id: 11264579 DOI: 10.1107/S0907444901001925

Date:

08-Mar-00 Release date: 08-Mar-01

Protein chains

O15382  (BCAT2_HUMAN) -  Branched-chain-amino-acid aminotransferase, mitochondrial from Homo sapiens

Seq: 392 a.a.

Struc: 365 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.6.1.42 - branched-chain-amino-acid transaminase.
• Pathway: Leucine Biosynthesis
• Reaction: L-leucine + 2-oxoglutarate = 4-methyl-2-oxopentanoate + L-glutamate
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

DOI no: 10.1107/S0907444901001925

Acta Crystallogr D Biol Crystallogr 57:506-515 (2001)

PubMed id: 11264579

The structure of human mitochondrial branched-chain aminotransferase.

N.Yennawar, J.Dunbar, M.Conway, S.Hutson, G.Farber.

ABSTRACT

X-ray crystal structures of three forms of human mitochondrial branched-chain aminotransferase (BCAT) were solved by molecular-replacement methods, using Escherichia coli BCAT as the search model. The enzyme is a homodimer and the polypeptide chain of each monomer has two domains. The small domain is composed of residues 1--175 and the large domain is composed of residues 176--365. The active site is close to the dimer interface. The 4'-aldehyde of the PLP cofactor is covalently linked to the epsilon-amino group of the active-site lysine, Lys202, via a Schiff-base linkage in two of the structures. In the third structure, the enzyme is irreversibly inactivated by Tris. The overall fold of the dimer in human mitochondrial BCAT is similar to the structure of two bacterial enzymes, E. coli BCAT and D-amino acid aminotransferase (D-AAT). The residues lining the putative substrate-binding pocket of human BCAT and D-AAT are completely rearranged to allow catalysis with substrates of opposite stereochemistry. In the case of human mitochondrial branched-chain aminotransferase, a hydrogen-bond interaction between the guanidinium group of Arg143 in the first monomer with the side-chain hydroxyl of Tyr70 in the second monomer is important in the formation of the substrate-binding pocket.

Selected figure(s)

Figure 2.
Figure 2 Active-site density of BCAT inhibited by Tris. The map was calculated from a structure that does not contain Tris. This is the first example in the Protein Data Bank where a buffer has formed a covalent intermediate with an enzyme active site.

Figure 6.
Figure 6 (a) Active-site superposition of E. coli BCAT (thinner bonds and smaller residue labels) with human BCATm (thicker bonds and larger residue labels). The side chains are conserved and their orientation is very similar. (b) Active-site superposition of D-AAT (thinner bonds and smaller residue labels) with human BCATm (thicker bonds and larger residue labels). Only the side chains interacting with the PLP are similar in nature and have comparable conformation.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 506-515) copyright 2001.

Figures were selected by the author.