Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography

Svensson, L.A.; Thulin, Eva; Forsén, Sture

doi:10.1016/0022-2836(92)90976-q

Cited by 143 publications

(155 citation statements)

References 31 publications

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“…The cis-trans isomerization of proline in a stably folded protein is not unique to CRL. It has been observed previously, e.g., in the crystal structure of calbindin Dgk, where a polypeptide stretch containing Pro 43 was found in 2 discrete conformations (Svenson et al, 1991). In solution, a mixture of cis and trans conformations of a proline was observed by NMR in several proteins, e.g., staphylococcal nuclease (Fox et al, 1986), insulin (Higgins et al, 1988), and calbindin D,, (Chazin et al, 1989).…”

Section: Discussionmentioning

confidence: 72%

Two conformational states of Candida rugosa lipase

et al. 1994

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The structure of Candida rugosa lipase in a new crystal form has been determined and refined at 2.1 A resolution. The lipase molecule was found in an inactive conformation, with the active site shielded from the solvent by a part of the polypeptide chain-the flap. Comparison of this structure with the previously determined "open" form of this lipase, in which the active site is accessible to the solvent and presumably the substrate, shows that the transition between these 2 states requires only movement of the flap. The backbone NH groups forming the putative oxyanion hole d o not change position during this rearrangement, indicating that this feature is preformed in the inactive state. The 2 lipase conformations probably correspond to states at opposite ends of the pathway of interfacial activation. Quantitative analysis indicates a large increase of the hydrophobic surface in the vicinity of the active site. The flap undergoes a flexible rearrangement during which some of its secondary structure refolds. The interactions of the flap with the rest of the protein change from mostly hydrophobic in the inactive form to largely hydrophilic in the "open" conformation. Although the flap movement cannot be described as a rigid body motion, it has very definite hinge points at Glu 66 and at Pro 92. The rearrangement is accompanied by a cis-trans isomerization of this proline, which likely increases the energy required for the transition between the 2 states, and may play a role in the stabilization of the active conformation at the water/lipid interface. Carbohydrate attached at Asn 351 also provides stabilization for the open conformation of the flap. Keywords: crystallography; interfacial activation; lipasesLipases of known 3-dimensional structure show significant similarities in their topologies and conform in full or in part to the a/fl hydrolase fold ( Ollis et al., 1992). The catalytic machinery of lipases consists of a serine protease-like triad, Ser-His-Asp/Glu, and their hydrolysis of ester bonds of triacylglycerols is thought to involve an enzymatic mechanism similar to that of the serine proteases (Chapus et al., 1988). The activity of lipases is dramatically enhanced by the presence of a lipid/water interface (Desnuelle, 1972), and it is now well accepted that the phenomenon of interfacial activation involves a conformational change in the enzyme. This has been documented for 2 lipases, one from Rhizomucor miehei (Brzozowski et ai., 199i) and another from human pancreas (van Tilbeurgh et al., 1993), in which binding of an inhibitor or substrate analog causes a conformational rearrangement of 1 or more loops near the active site, exposing the serine nucleophile to the solvent and creating also an oxyanion hole in the process.A similar rearrangement was also proposed for larger lipases from Geotrichum candidurn (GCL;Schrag & Cygler, 1993) Candida rugosa (CRL; Grochubki et ai., 1993). These 2 enzymes show -40% amino acid sequence identity, and their overall 3D structures are very similar (Grochulski ...

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Section: Discussionmentioning

confidence: 72%

Two conformational states of Candida rugosa lipase

et al. 1994

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“…calbindin D 9K (98), calmodulin (99), troponin C (100, 101), SCBP (102), and recoverin (103)) or by NMR spectroscopy (e.g. calbindin D 9K (104,105), homo-and heterodimers of Ca 2ϩ binding sites of the C-domain of troponin C (106 -108), N-domain of troponin C (109), C-domain of calmodulin and intact calmodulin (110 -112), spectrin (113), S100b (114), calcyclin (115), and recoverin (116)).…”

Section: Helix-loop-helix Ca 2؉ Binding Motifsmentioning

confidence: 99%

α-Helical Protein Assembly Motifs

Kohn

Mant

Hodges

1997

Journal of Biological Chemistry

184

132

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“…4. Precedence for this type of isomerism has been observed by X-ray crystallography for Gly42-Pro43 of calbindin D,, [33]. This CD4 induced shift would provide a mechanism for presentation of the V, loop as a competent 'trypsin-like' substrate to a cellular protease for activation for subsequent membrane fusion.…”

Section: Discussionmentioning

confidence: 90%

Conformational rearrangements required of the V₃ loop of HIV‐1 gp120 for proteolytic cleavage and infection

et al. 1994

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HIV gp120 is specifically cleaved at a single site in the V, loop between Arg315 and Ala316 by thrombin. Previous observations by others have indicated that binding to CD4 enhances the rate of Vg loop cleavage, and that this cleavage is a prerequisite for HIV infection. Other observations also suggest that the cleavage site is in a type II B-turn centered at Pro313 -Gly314. However, our docking experiments indicate that this conformation cannot dock to thrombin and other trypsin-like serine proteases. Thus, based on the thrombin-bound conformation of peptide substrates, we propose that CD4 binding, at a site remote from the V, loop, induces and stabilizes a trans to cis isomerization of the highly conserved residue Pro"', and that this conformational shift is a prerequisite for cleavage by a 'thrombin-like' cellular protease and subsequent infection.

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Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography

Cited by 143 publications

References 31 publications

Two conformational states of Candida rugosa lipase

Two conformational states of Candida rugosa lipase

α-Helical Protein Assembly Motifs

Conformational rearrangements required of the V₃ loop of HIV‐1 gp120 for proteolytic cleavage and infection

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Proline cis-trans isomers in calbindin D9k observed by X-ray crystallography

Cited by 143 publications

References 31 publications

Two conformational states of Candida rugosa lipase

Two conformational states of Candida rugosa lipase

α-Helical Protein Assembly Motifs

Conformational rearrangements required of the V3 loop of HIV‐1 gp120 for proteolytic cleavage and infection

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Conformational rearrangements required of the V₃ loop of HIV‐1 gp120 for proteolytic cleavage and infection