The Structural Determination of an Insect Sterol Carrier Protein-2 with a Ligand-bound C16 Fatty Acid at 1.35-Å Resolution

Dyer, David H.; Lovell, Scott; Thoden, James B.; Holden, Hazel M.; Rayment, Ivan; Lan, Qing

doi:10.1074/jbc.m306214200

Cited by 79 publications

(135 citation statements)

References 41 publications

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“…Each of the four variants, regardless of the presence or absence of either presequence or PTS1, were found by far-UV CD to be natively folded, as estimated by far-UV CD and confirming previous structural data [3,13,26,[29][30][31]. Previous spectroscopic studies [32,33] have shown that the presequence of SCP2 does not display regular secondary structure-a conclusion confirmed by the CD data presented here.…”

Section: Discussionsupporting

confidence: 90%

“…[26,30,31] in which the C-terminal segment of SCP2 is found to be in a coiled conformation. Crystal structures of liganded SCP2 [13,29] show the C-terminal segment adopting an a-helical structure ''capping'' the ligand binding pocket. This coil-helix transition upon ligand binding may to some degree explain the ''tightening'' of secondary structure we observe when SCP2 is loaded with stearoyl CoA.…”

Section: Discussionmentioning

confidence: 99%

“…1b). In the available crystal structure of mosquito SCP2 in complex with palmitic acid [13], one carboxylate oxygen of palmitic acid is buried within SCP2 (Fig. 8a)-hydrogen bonding directly with three residues: Arg24, Gln25 and Val26.…”

Section: Discussionmentioning

confidence: 99%

“…8a)-hydrogen bonding directly with three residues: Arg24, Gln25 and Val26. The other carboxylate oxygen, however, is solvent exposed, hydrogen bonding with Arg15 and Asp20 via water molecules [13]. It could be expected that bound LCFA-CoAs will have the head group-fatty acid thioester linkage at this position.…”

Section: Discussionmentioning

confidence: 99%

“…Amongst the numerous ligands of SCP2 are LCFAs (discussed extensively in [10,11] with structural analysis in [12,13]) and LCFA-CoAs [14][15][16][17][18] as well as a number of intermediates of LCFA b-oxidation-a primary function of the peroxisome [16]. In addition to the high affinity for these ligands, the observed direct association of peroxisomal SCP2 with b-oxidation enzymes acyl CoA oxidase, thiolase A and MFE-2 [19] has led to the suggestion that a function of SCP2 is to stabilise LCFA b-oxidation intermediates and to present them to the appropriate enzymes for further processing (reviewed in [20]).…”

mentioning

confidence: 99%

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Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

Stanley

Versluis

Schultz

et al. 2007

Archives of Biochemistry and Biophysics

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Sterol carrier protein 2 (SCP2) has been investigated by nearly native electrospray ionisation mass spectrometry in the presence of long chain fatty acyl CoAs (LCFA-CoAs) and carnitine derivatives of equivalent fatty acid chain length (LCFA-carnitines). Four SCP2 constructs were compared to examine the influence of the N-terminal presequence and the C-terminal peroxisomal targeting signal on ligand binding. Removal of N-or C-terminal residues did not influence ligand binding. The observation that LCFA-CoAs are high affinity ligands for SCP2 was confirmed, while LCFA-carnitines were demonstrated for the first time not to interact with SCP2. LCFACoAs formed non-covalent complexes with SCP2 of 2:1 and 1:1 stoichiometry, which could be dissociated by elevating the energy of the ions upon entrance to the mass spectrometer. A fluorescence-competition assay using Nile Red butyric acid confirmed the mass spectrometric observations in solution. The physiological significance of the lack of LCFA-carnitine binding by SCP2 is discussed.

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Section: Discussionsupporting

confidence: 90%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

Stanley

Versluis

Schultz

et al. 2007

Archives of Biochemistry and Biophysics

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3₁₀‐helices in proteins are parahelices

et al. 2006

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The 3(10)-helix is characterized by having at least two consecutive hydrogen bonds between the main-chain carbonyl oxygen of residue i and the main-chain amide hydrogen of residue i + 3. The helical parameters--pitch, residues per turn, radius, and root mean square deviation (rmsd) from the best-fit helix--were determined by using the HELFIT program. All 3(10)-helices were classified as regular or irregular based on rmsd/(N - 1)1/2 where N is the helix length. For both there are systematic, position-specific shifts in the backbone dihedral angles. The average phi, psi shift systematically from approximately -58 degrees, approximately -32 degrees to approximately -90 degrees, approximately -4 degrees for helices 5, 6, and 7 residues long. The same general pattern is seen for helices, N = 8 and 9; however, in N = 9, the trend is repeated with residues 6, 7, and 8 approximately repeating the phi, psi of residues 2, 3, and 4. The residues per turn and radius of regular 3(10)-helices decrease with increasing length of helix, while the helix pitch and rise per residue increase. That is, regular 3(10)-helices become thinner and longer as N increases from 5 to 8. The fraction of regular 3(10)-helices decreases linearly with helix length. All longer helices, N > or = 9 are irregular. Energy minimizations show that regular helices become less stable with increasing helix length. These findings indicate that the definition of 3(10)-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 3(10)-helix. The 3(10)-helices observed in proteins are better referred to parahelices.

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High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl‐CoA ligand

et al. 2006

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The acyl-CoA binding protein (ACBP) is essential for the fatty acid metabolism, membrane structure, membrane fusion, and ceramide synthesis. Here high resolution crystal structures of human cytosolic liver ACBP, unliganded and liganded with a physiological ligand, myristoyl-CoA are described. The binding of the acyl-CoA molecule induces only few structural differences near the binding pocket. The crystal form of the liganded ACBP, which has two ACBP molecules in the asymmetric unit, shows that in human ACBP the same acyl-CoA binding pocket is present as previously described for the bovine and Plasmodium falciparum ACBP and the mode of binding of the 3 0 -phosphate-AMP moiety is conserved. Unexpectedly, in one of the acyl-CoA binding pockets the acyl moiety is bound in a reversed mode as compared with the bovine and P. falciparum structures. In this binding mode, the myristoyl-CoA molecule is fully ordered and bound across the two ACBP molecules of the crystallographic asymmetric unit: the 3 0 -phosphate-AMP moiety is bound in the binding pocket of one ACBP molecule and the acyl chain is bound in the pocket of the other ACBP molecule. The remaining binding pocket cavities of these two ACBP molecules are filled by other ligand fragments. This novel binding mode shows that the acyl moiety can flip out of its classical binding pocket and bind elsewhere, suggesting a mechanism for the acyl-CoA transfer between ACBP and the active site of a target enzyme. This mechanism is of possible relevance for the in vivo function of ACBP.

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The Structural Determination of an Insect Sterol Carrier Protein-2 with a Ligand-bound C16 Fatty Acid at 1.35-Å Resolution

Cited by 79 publications

References 41 publications

Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

3₁₀‐helices in proteins are parahelices

High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl‐CoA ligand

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The Structural Determination of an Insect Sterol Carrier Protein-2 with a Ligand-bound C16 Fatty Acid at 1.35-Å Resolution

Cited by 79 publications

References 41 publications

Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

Investigation of the ligand spectrum of human sterol carrier protein 2 using a direct mass spectrometry assay

310‐helices in proteins are parahelices

High resolution crystal structures of unliganded and liganded human liver ACBP reveal a new mode of binding for the acyl‐CoA ligand

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3₁₀‐helices in proteins are parahelices