1dpe
From Proteopedia
(New page: 200px<br /><applet load="1dpe" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dpe, resolution 2.0Å" /> '''DIPEPTIDE-BINDING PRO...) |
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| - | [[Image:1dpe.jpg|left|200px]]<br /><applet load="1dpe" size=" | + | [[Image:1dpe.jpg|left|200px]]<br /><applet load="1dpe" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1dpe, resolution 2.0Å" /> | caption="1dpe, resolution 2.0Å" /> | ||
'''DIPEPTIDE-BINDING PROTEIN'''<br /> | '''DIPEPTIDE-BINDING PROTEIN'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The family of about 50 periplasmic binding proteins, which exhibit diverse | + | The family of about 50 periplasmic binding proteins, which exhibit diverse specificity (e.g., carbohydrates, amino acids, dipeptides, oligopeptides, oxyanions, metals, and vitamins) and range in size from 20 to 58 kDa, is a gold mine for an atomic-level investigation of structure and molecular recognition. These proteins serve as initial receptors for active transport systems or permeases. About six of these proteins, including the dipeptide-binding protein (DppA), are also primary receptors for chemotaxis. The structure of the unbound form of DppA (M(r) = 57,400) has been determined and refined to an R-factor of 0.169 to 2 A resolution. DppA consists of two distinct domains (I and II) connected by two "hinge" segments which form part of the base of the wide groove between the two domains. The relative orientation of the two domains gives the protein a pearlike shape, with domain I and domain II forming the larger and smaller apical ends, respectively. From the tip to the rounded bottom measures about 85 A, and the widest diameter is about 60 A. Domain I, which consists of two integrated subdomains, is folded from two separate polypeptide segments from the amino- and carboxyl-terminal ends. The more compact domain II is formed from the intervening segment. Comparison of the dipeptide-binding protein structure with that of the bound form of the similar oligopeptide-binding protein [Tame, J. R. H., Murshudov, G. N., Dodson, E. J., Neil, T. K., Dodson, G. G., Higgins, C. F., & Wilkinson, A. J. (1994) Science 264, 1578-1581] reveals the major features that differentiate the ligand specificity of the two proteins and describe the large hinge bending (about 55 degrees) between the two domains. |
==About this Structure== | ==About this Structure== | ||
| - | 1DPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with CD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 1DPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=CD:'>CD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DPE OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: Nickitenko, A | + | [[Category: Nickitenko, A V.]] |
| - | [[Category: Quiocho, F | + | [[Category: Quiocho, F A.]] |
[[Category: Trakhanov, S.]] | [[Category: Trakhanov, S.]] | ||
[[Category: CD]] | [[Category: CD]] | ||
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[[Category: periplasmic]] | [[Category: periplasmic]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:19:03 2008'' |
Revision as of 10:19, 21 February 2008
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DIPEPTIDE-BINDING PROTEIN
Overview
The family of about 50 periplasmic binding proteins, which exhibit diverse specificity (e.g., carbohydrates, amino acids, dipeptides, oligopeptides, oxyanions, metals, and vitamins) and range in size from 20 to 58 kDa, is a gold mine for an atomic-level investigation of structure and molecular recognition. These proteins serve as initial receptors for active transport systems or permeases. About six of these proteins, including the dipeptide-binding protein (DppA), are also primary receptors for chemotaxis. The structure of the unbound form of DppA (M(r) = 57,400) has been determined and refined to an R-factor of 0.169 to 2 A resolution. DppA consists of two distinct domains (I and II) connected by two "hinge" segments which form part of the base of the wide groove between the two domains. The relative orientation of the two domains gives the protein a pearlike shape, with domain I and domain II forming the larger and smaller apical ends, respectively. From the tip to the rounded bottom measures about 85 A, and the widest diameter is about 60 A. Domain I, which consists of two integrated subdomains, is folded from two separate polypeptide segments from the amino- and carboxyl-terminal ends. The more compact domain II is formed from the intervening segment. Comparison of the dipeptide-binding protein structure with that of the bound form of the similar oligopeptide-binding protein [Tame, J. R. H., Murshudov, G. N., Dodson, E. J., Neil, T. K., Dodson, G. G., Higgins, C. F., & Wilkinson, A. J. (1994) Science 264, 1578-1581] reveals the major features that differentiate the ligand specificity of the two proteins and describe the large hinge bending (about 55 degrees) between the two domains.
About this Structure
1DPE is a Single protein structure of sequence from Escherichia coli with as ligand. Full crystallographic information is available from OCA.
Reference
2 A resolution structure of DppA, a periplasmic dipeptide transport/chemosensory receptor., Nickitenko AV, Trakhanov S, Quiocho FA, Biochemistry. 1995 Dec 26;34(51):16585-95. PMID:8527431
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