PDBsum entry 2evb

Lipid binding protein,transferase

PDB id: 2evb

Contents

Protein chain

74 a.a. *

Waters ×111

* Residue conservation analysis

PDB id:

2evb

Name:

Lipid binding protein,transferase

Title:

Structure of biotin carboxyl carrier protein (74val start) from pyrococcus horikoshi ot3 ligand free form i

Structure:

Methylmalonyl-coa decarboxylase gamma chain. Chain: a. Fragment: residues 73-146. Synonym: biotin carboxyl carrier protein. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: bccp. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.55Å R-factor: 0.248 R-free: 0.283

Authors:

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

Key ref:

B.Bagautdinov et al. (2008). Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate. J Biol Chem, 283, 14739-14750. PubMed id: 18372281 DOI: 10.1074/jbc.M709116200

Date:

31-Oct-05 Release date: 01-May-06

Protein chain

O59021  (O59021_PYRHO) -  149aa long hypothetical methylmalonyl-CoA decarboxylase gamma chain from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 149 a.a.

Struc: 74 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.2.1.3.1 - methylmalonyl-CoA carboxytransferase.
• Reaction: (S)-methylmalonyl-CoA + pyruvate = propanoyl-CoA + oxaloacetate
• Cofactor: Biotin; Cobalt cation; Zn(2+)

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

reference

DOI no: 10.1074/jbc.M709116200

J Biol Chem 283:14739-14750 (2008)

PubMed id: 18372281

Protein biotinylation visualized by a complex structure of biotin protein ligase with a substrate.

B.Bagautdinov, Y.Matsuura, S.Bagautdinova, N.Kunishima.

ABSTRACT

Biotin protein ligase (BPL) catalyzes the biotinylation of the biotin carboxyl carrier protein (BCCP) only at a special lysine residue. Here we report the first structure of BPL.BCCP complex crystals, which are prepared using two BPL mutants: R48A and R48A/K111A. From a detailed structural characterization, it is likely that the mutants retain functionality as enzymes but have a reduced activity to produce the reaction intermediate biotinyl-5'-AMP. The observed biotin and partly disordered ATP in the mutant structures may act as a non-reactive analog of the substrates or biotinyl-5'-AMP, thereby providing the complex crystals. The four crystallographically independent BPL.BCCP complexes obtained can be classified structurally into three groups: the formation stages 1 and 2 with apo-BCCP and the product stage with biotinylated holo-BCCP. Residues responsible for the complex formation as well as for the biotinylation reaction have been identified. The C-terminal domain of BPL shows especially large conformational changes to accommodate BCCP, suggesting its functional importance. The formation stage 1 complex shows the closest distance between the carboxyl carbon of biotin and the special lysine of BCCP, suggesting its relevance to the unobserved reaction stage. Interestingly, bound ATP and biotin are also seen in the product stage, indicating that the substrates may be recruited into the product stage complex before the release of holo-BCCP, probably for the next reaction cycle. The existence of formation and product stages before and after the reaction stage would be favorable to ensure both the reaction efficiency and the extreme substrate specificity of the biotinylation reaction.

Selected figure(s)

Figure 3.
FIGURE 3. Interface charge distribution in the double mutant complex. The formation stage 1 complex observed in the B and D subunits is presented. Electrostatic potential surface representation for PhBPL (blue and red colors correspond to positive and negative potentials, respectively) and ribbon representation for PhBCCP are used. The buried residues of PhBCCP at the protein·protein interface are shown as stick models.

Figure 5.
FIGURE 5. Enlarged stereo representation showing intermolecular interactions in the double mutant complex. Residues involved in the intermolecular direct hydrogen bonds (2.2-3.5 Å) are shown in stick models and labeled. The hydrogen bonds are indicated by red dotted lines. A, subunits B and D in the formation stage 1; B, subunits A and C in the product stage.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 14739-14750) copyright 2008.

Figures were selected by an automated process.