PDBsum entry: 1bdo

Transferase

PDB id: 1bdo

Contents

Protein chain

80 a.a. *

Ligands

BTN

Waters ×74

* Residue conservation analysis

PDB id:

1bdo

Name:

Transferase

Title:

Structure of the biotinyl domain of acetyl-coenzyme a carbox determined by mad phasing

Structure:

Acetyl-coa carboxylase. Chain: a. Fragment: biotinyl domain, residues 77 - 156. Synonym: functional fragment of biotin carboxyl carrier pro bccpsc. Engineered: yes. Other_details: bccpsc is obtained by digesting recombinant carboxyl carrier protein with subtilisin carlsberg

Source:

Escherichia coli. Organism_taxid: 562. Gene: biotin carboxyl carrier protei. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: the fragment bccpsc, residues 77-156, is obt digesting the expressed recombinant protein with subtilisin carlsberg

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.189

Authors:

F.K.Athappilly,W.A.Hendrickson

Key ref:

F.K.Athappilly and W.A.Hendrickson (1995). Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing. Structure, 3, 1407-1419. PubMed id: 8747466 DOI: 10.1016/S0969-2126(01)00277-5

Date:

21-Nov-95 Release date: 01-Aug-96

Protein chain

P0ABD8  (BCCP_ECOLI) -  Biotin carboxyl carrier protein of acetyl-CoA carboxylase

Seq: 156 a.a.

Struc: 80 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: acetyl-CoA carboxylase complex (1 term)
• Biological process: fatty acid biosynthetic process (1 term)
• Biochemical function: acetyl-CoA carboxylase activity (1 term)

DOI no: 10.1016/S0969-2126(01)00277-5

Structure 3:1407-1419 (1995)

PubMed id: 8747466

Structure of the biotinyl domain of acetyl-coenzyme A carboxylase determined by MAD phasing.

F.K.Athappilly, W.A.Hendrickson.

ABSTRACT

BACKGROUND: Acetyl-coenzyme A carboxylase catalyzes the first committed step of fatty acid biosynthesis. Universally, this reaction involves three functional components all related to a carboxybiotinyl intermediate. A biotinyl domain shuttles its covalently attached biotin prosthetic group between the active sites of a biotin carboxylase and a carboxyl transferase. In Escherichia coli, the three components reside in separate subunits: a biotinyl domain is the functional portion of one of these, biotin carboxy carrier protein (BCCP). RESULTS: We have expressed natural and selenomethionyl (Se-met) BCCP from E. coli as biotinylated recombinant proteins, proteolyzed them with subtilisin Carlsberg to produce the biotinyl domains BCCP and Se-met BCCPsc, determined the crystal structure of Se-met BCCPsc using a modified version of the multiwavelength anomalous diffraction (MAD) phasing protocol, and refined the structure for the natural BCCPsc at 1.8 A resolution. The structure may be described as a capped beta sandwich with quasi-dyad symmetry. Each half contains a characteristic hammerhead motif. The biotinylated lysin is located at a hairpin beta turn which connects the two symmetric halves of the molecule, and its biotinyl group interacts with a non-symmetric protrusion from the core. CONCLUSIONS: This first crystal structure of a biotinyl domain helps to unravel the central role of such domains in reactions catalyzed by biotin-dependent carboxylases. The hammerhead structure observed twice in BCCPsc may be regarded as the basic structural motif of biotinyl and lipoyl domains of a superfamily of enzymes. The new MAD phasing techniques developed in the course of determining this structure enhance the power of the MAD method.

Selected figure(s)

Figure 1.
Figure 1. . Overall folding of BCCP[sc]. (a) A ribbon diagram of BCCP[sc]. The side chain of biocytin is shown in ball-and-stick representation with carbon, nitrogen, oxygen and sulfur atoms colored green, blue, red, and yellow respectively. The β strands are labeled. The direction of view is along the intramolecular quasi-dyad axis of symmetry. (b) A stereo view of the Cα trace of BCCP[sc] in the same orientation as in (a). Every tenth residue is numbered and is indicated by a filled circle on the Cα atom. (Figure prepared using MOLSCRIPT [66].). Figure 1. . Overall folding of BCCP[sc]. (a) A ribbon diagram of BCCP[sc]. The side chain of biocytin is shown in ball-and-stick representation with carbon, nitrogen, oxygen and sulfur atoms colored green, blue, red, and yellow respectively. The β strands are labeled. The direction of view is along the intramolecular quasi-dyad axis of symmetry. (b) A stereo view of the Cα trace of BCCP[sc] in the same orientation as in (a). Every tenth residue is numbered and is indicated by a filled circle on the Cα atom. (Figure prepared using MOLSCRIPT [[4]66].).

Figure 7.
Figure 7. . Superposition of the Cα backbones of BCCP[sc] (red), lipoylated H-protein from pGD (green) [17] and the lipoyl domain from bPD (blue) [15]. In the case of pGD, only residues 19–108 were used in this superposition. See Figure 8 for the residues of pGD and bPD used to calculate the superposition matrices. (Figure prepared using MOLSCRIPT [66].). Figure 7. . Superposition of the Cα backbones of BCCP[sc] (red), lipoylated H-protein from pGD (green) [[3]17] and the lipoyl domain from bPD (blue) [[4]15]. In the case of pGD, only residues 19–108 were used in this superposition. See [5]Figure 8 for the residues of pGD and bPD used to calculate the superposition matrices. (Figure prepared using MOLSCRIPT [[6]66].).

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1407-1419) copyright 1995.

Figures were selected by an automated process.