PDBsum entry 2jku

Ligase

PDB id: 2jku

Contents

Protein chain

35 a.a. *

Ligands

PG4 ×2

Waters ×58

* Residue conservation analysis

PDB id:

2jku

Name:

Ligase

Title:

Crystal structure of the n-terminal region of the biotin acceptor domain of human propionyl-coa carboxylase

Structure:

Propionyl-coa carboxylase alpha chain, mitochondrial. Chain: a. Fragment: biotin acceptor domain, residues 633-703. Synonym: propanoyl-coa\:carbon dioxide ligase subunit alpha. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organelle: mitochondria. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: r3-prare2.

Resolution:

1.50Å R-factor: 0.149 R-free: 0.166

Authors:

S.Healy,W.W.Yue,G.Kochan,E.S.Pilka,J.W.Murray,A.K.Roos, P.Filippakopoulos,F.Von Delft,C.Arrowsmith,M.Wikstrom,A.Edwards, C.Bountra,R.A.Gravel,U.Oppermann

Key ref:

S.Healy et al. (2010). Structural impact of human and Escherichia coli biotin carboxyl carrier proteins on biotin attachment. Biochemistry, 49, 4687-4694. PubMed id: 20443544

Date:

30-Aug-08 Release date: 09-Sep-08

Protein chain

P05165  (PCCA_HUMAN) -  Propionyl-CoA carboxylase alpha chain, mitochondrial from Homo sapiens

Seq: 728 a.a.

Struc: 35 a.a.

Enzyme reactions

• Enzyme class: E.C.6.4.1.3 - propionyl-CoA carboxylase.
• Reaction: propanoyl-CoA + hydrogencarbonate + ATP = (S)-methylmalonyl-CoA + ADP + phosphate + H⁺
• Cofactor: Biotin

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

reference

Biochemistry 49:4687-4694 (2010)

PubMed id: 20443544

Structural impact of human and Escherichia coli biotin carboxyl carrier proteins on biotin attachment.

S.Healy, M.K.McDonald, X.Wu, W.W.Yue, G.Kochan, U.Oppermann, R.A.Gravel.

ABSTRACT

Holocarboxylase synthetase (HCS, human) and BirA (Escherichia coli) are biotin protein ligases that catalyze the ATP-dependent attachment of biotin to apocarboxylases. Biotin attachment occurs on a highly conserved lysine residue within a consensus sequence (Ala/Val-Met-Lys-Met) that is found in carboxylases in most organisms. Numerous studies have indicated that HCS and BirA, as well as biotin protein ligases from other organisms, can attach biotin to apocarboxylases from different organisms, indicating that the mechanism of biotin attachment is well conserved. In this study, we examined the cross-reactivity of biotin attachment between human and bacterial biotin ligases by comparing biotinylation of p-67 and BCCP87, the biotin-attachment domain fragments from human propionyl-CoA carboxylase and E. coli acetyl-CoA carboxylase, respectively. While BirA has similar biotinylation activity toward the two substrates, HCS has reduced activity toward bacterial BCCP87 relative to its native substrate, p-67. The crystal structure of a digested form of p-67, spanning a sequence that contains a seven-residue protruding thumb loop in BCCP87, revealed the absence of a similar structure in the human peptide. Significantly, an engineered "thumbless" bacterial BCCP87 could be biotinylated by HCS, with substrate affinity restored to near normal. This study suggests that the thumb loop found in bacterial carboxylases interferes with optimal interaction with the mammalian biotin protein ligase. While the function of the thumb loop remains unknown, these results indicate a constraint on specificity of the bacterial substrate for biotin attachment that is not itself a feature of BirA.