2psg
From Proteopedia
(New page: 200px<br /><applet load="2psg" size="450" color="white" frame="true" align="right" spinBox="true" caption="2psg, resolution 1.8Å" /> '''REFINED STRUCTURE OF ...) |
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| - | [[Image:2psg.gif|left|200px]]<br /><applet load="2psg" size=" | + | [[Image:2psg.gif|left|200px]]<br /><applet load="2psg" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2psg, resolution 1.8Å" /> | caption="2psg, resolution 1.8Å" /> | ||
'''REFINED STRUCTURE OF PORCINE PEPSINOGEN AT 1.8 ANGSTROMS RESOLUTION'''<br /> | '''REFINED STRUCTURE OF PORCINE PEPSINOGEN AT 1.8 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The molecular structure of porcine pepsinogen at 1.8 A resolution has been | + | The molecular structure of porcine pepsinogen at 1.8 A resolution has been determined by a combination of molecular replacement and multiple isomorphous phasing techniques. The resulting structure was refined by restrained-parameter least-squares methods. The final R factor [formula: see text] is 0.164 for 32,264 reflections with I greater than or equal to sigma (I) in the resolution range of 8.0 to 1.8 A. The model consists of 2785 protein atoms in 370 residues, a phosphoryl group on Ser68 and 238 ordered water molecules. The resulting molecular stereochemistry is consistent with a well-refined crystal structure with co-ordinate accuracy in the range of 0.10 to 0.15 A for the well-ordered regions of the molecule (B less than 15 A2). For the enzyme portion of the zymogen, the root-mean-square difference in C alpha atom co-ordinates with the refined porcine pepsin structure is 0.90 A (284 common atoms) and with the C alpha atoms of penicillopepsin it is 1.63 A (275 common atoms). The additional 44 N-terminal amino acids of the prosegment (Leu1p to Leu44p, using the letter p after the residue number to distinguish the residues of the prosegment) adopt a relatively compact structure consisting of a long beta-strand followed by two approximately orthogonal alpha-helices and a short 3(10)-helix. Intimate contacts, both electrostatic and hydrophobic interactions, are made with residues in the pepsin active site. The N-terminal beta-strand, Leu1p to Leu6p, forms part of the six-stranded beta-sheet common to the aspartic proteinases. In the zymogen the first 13 residues of pepsin, Ile1 to Glu13, adopt a completely different conformation from that of the mature enzyme. The C alpha atom of Ile1 must move approximately 44 A in going from its position in the inactive zymogen to its observed position in active pepsin. Electrostatic interactions of Lys36pN and hydrogen-bonding interactions of Tyr37pOH, and Tyr90H with the two catalytic aspartate groups, Asp32 and Asp215, prevent substrate access to the active site of the zymogen. We have made a detailed comparison of the mammalian pepsinogen fold with the fungal aspartic proteinase fold of penicillopepsin, used for the molecular replacement solution. A structurally derived alignment of the two sequences is presented. |
==About this Structure== | ==About this Structure== | ||
| - | 2PSG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with PO3 as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | + | 2PSG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=PO3:'>PO3</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PSG OCA]. |
==Reference== | ==Reference== | ||
Refined structure of porcine pepsinogen at 1.8 A resolution., Sielecki AR, Fujinaga M, Read RJ, James MN, J Mol Biol. 1991 Jun 20;219(4):671-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2056534 2056534] | Refined structure of porcine pepsinogen at 1.8 A resolution., Sielecki AR, Fujinaga M, Read RJ, James MN, J Mol Biol. 1991 Jun 20;219(4):671-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=2056534 2056534] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
| - | [[Category: James, M | + | [[Category: James, M N.G.]] |
| - | [[Category: Sielecki, A | + | [[Category: Sielecki, A R.]] |
[[Category: PO3]] | [[Category: PO3]] | ||
[[Category: hydrolase(acid proteinase zymogen)]] | [[Category: hydrolase(acid proteinase zymogen)]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:32:35 2008'' |
Revision as of 16:32, 21 February 2008
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REFINED STRUCTURE OF PORCINE PEPSINOGEN AT 1.8 ANGSTROMS RESOLUTION
Overview
The molecular structure of porcine pepsinogen at 1.8 A resolution has been determined by a combination of molecular replacement and multiple isomorphous phasing techniques. The resulting structure was refined by restrained-parameter least-squares methods. The final R factor [formula: see text] is 0.164 for 32,264 reflections with I greater than or equal to sigma (I) in the resolution range of 8.0 to 1.8 A. The model consists of 2785 protein atoms in 370 residues, a phosphoryl group on Ser68 and 238 ordered water molecules. The resulting molecular stereochemistry is consistent with a well-refined crystal structure with co-ordinate accuracy in the range of 0.10 to 0.15 A for the well-ordered regions of the molecule (B less than 15 A2). For the enzyme portion of the zymogen, the root-mean-square difference in C alpha atom co-ordinates with the refined porcine pepsin structure is 0.90 A (284 common atoms) and with the C alpha atoms of penicillopepsin it is 1.63 A (275 common atoms). The additional 44 N-terminal amino acids of the prosegment (Leu1p to Leu44p, using the letter p after the residue number to distinguish the residues of the prosegment) adopt a relatively compact structure consisting of a long beta-strand followed by two approximately orthogonal alpha-helices and a short 3(10)-helix. Intimate contacts, both electrostatic and hydrophobic interactions, are made with residues in the pepsin active site. The N-terminal beta-strand, Leu1p to Leu6p, forms part of the six-stranded beta-sheet common to the aspartic proteinases. In the zymogen the first 13 residues of pepsin, Ile1 to Glu13, adopt a completely different conformation from that of the mature enzyme. The C alpha atom of Ile1 must move approximately 44 A in going from its position in the inactive zymogen to its observed position in active pepsin. Electrostatic interactions of Lys36pN and hydrogen-bonding interactions of Tyr37pOH, and Tyr90H with the two catalytic aspartate groups, Asp32 and Asp215, prevent substrate access to the active site of the zymogen. We have made a detailed comparison of the mammalian pepsinogen fold with the fungal aspartic proteinase fold of penicillopepsin, used for the molecular replacement solution. A structurally derived alignment of the two sequences is presented.
About this Structure
2PSG is a Single protein structure of sequence from [1] with as ligand. Full crystallographic information is available from OCA.
Reference
Refined structure of porcine pepsinogen at 1.8 A resolution., Sielecki AR, Fujinaga M, Read RJ, James MN, J Mol Biol. 1991 Jun 20;219(4):671-92. PMID:2056534
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