PDBsum entry 1wpy

Ligase

PDB id: 1wpy

Contents

Protein chains

235 a.a. *

Ligands

BTN ×2

Waters ×638

* Residue conservation analysis

PDB id:

1wpy

Name:

Ligase

Title:

Crystal structure of biotin-(acetyl-coa-carboxylase) ligase from pyrococcus horikoshii ot3 in complex with biotin

Structure:

Biotin--[acetyl-coa-carboxylase] ligase. Chain: a, b. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: bira. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.60Å R-factor: 0.194 R-free: 0.213

Authors:

B.Bagautdinov,N.Kunishima,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

B.Bagautdinov et al. (2005). Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation. J Mol Biol, 353, 322-333. PubMed id: 16169557 DOI: 10.1016/j.jmb.2005.08.032

Date:

17-Sep-04 Release date: 04-Oct-05

Protein chains

O57883  (O57883_PYRHO) -  235aa long hypothetical biotin--[acetyl-CoA-carboxylase] ligase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 235 a.a.

Struc: 235 a.a.

Enzyme reactions

• Enzyme class: E.C.6.3.4.15 - biotin--[biotin carboxyl-carrier protein] ligase.
• Reaction: biotin + L-lysyl-[protein] + ATP = N₆-biotinyl-L-lysyl-[protein] + AMP + diphosphate + H⁺

biotin + L-lysyl-[protein] (Bound ligand (Het Group name = BTN) corresponds exactly) + ATP = N(6)-biotinyl-L-lysyl-[protein] + AMP + diphosphate + H(+)

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

reference

DOI no: 10.1016/j.jmb.2005.08.032

J Mol Biol 353:322-333 (2005)

PubMed id: 16169557

Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation.

B.Bagautdinov, C.Kuroishi, M.Sugahara, N.Kunishima.

ABSTRACT

Biotin protein ligase (EC 6.3.4.15) catalyses the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. The three-dimensional structure of biotin protein ligase from Pyrococcus horikoshii OT3 has been determined by X-ray diffraction at 1.6A resolution. The structure reveals a homodimer as the functional unit. Each subunit contains two domains, a larger N-terminal catalytic domain and a smaller C-terminal domain. The structural feature of the active site has been studied by determination of the crystal structures of complexes of the enzyme with biotin, ADP and the reaction intermediate biotinyl-5'-AMP at atomic resolution. This is the first report of the liganded structures of biotin protein ligase with nucleotide and biotinyl-5'-AMP. The structures of the unliganded and the liganded forms are isomorphous except for an ordering of the active site loop upon ligand binding. Catalytic binding sites are suitably arranged to minimize the conformational changes required during the reaction, as the pockets for biotin and nucleotide are located spatially adjacent to each other in a cleft of the catalytic domain and the pocket for biotinyl-5'-AMP binding mimics the combination of those of the substrates. The exact locations of the ligands and the active site residues allow us to propose a general scheme for the first step of the reaction carried out by biotin protein ligase in which the positively charged epsilon-amino group of Lys111 facilitates the nucleophilic attack on the ATP alpha-phosphate group by the biotin carboxyl oxygen atom and stabilizes the negatively charged intermediates.

Selected figure(s)

Figure 6.
Figure 6. Charge distribution of the molecular surface of the biotinyl-5'-AMP liganded form. Negatively and positively charged surfaces are coloured red and blue, respectively. The active site architecture fits well for the ligase reaction intermediate, biotinyl-5'-AMP, with its ureido and tetrahydrothiophene rings of biotinyl moiety bound deep into the cleft. The active site residues are labelled.

Figure 7.
Figure 7. Hydrogen bonding interactions (within 3.5 Å) between the protein and (a) biotin, (b) ADP and (c) biotinyl-5'-AMP, as indicated by the broken lines with distances in Å. Relevant amino acids with hydrogen bonds are shown. The relevant ligand atoms involved in the interactions are labelled.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 322-333) copyright 2005.

Figures were selected by an automated process.