2psg
From Proteopedia
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|PDB= 2psg |SIZE=350|CAPTION= <scene name='initialview01'>2psg</scene>, resolution 1.8Å | |PDB= 2psg |SIZE=350|CAPTION= <scene name='initialview01'>2psg</scene>, resolution 1.8Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=PO3:PHOSPHITE ION'>PO3</scene> | + | |LIGAND= <scene name='pdbligand=PO3:PHOSPHITE+ION'>PO3</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2psg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2psg OCA], [http://www.ebi.ac.uk/pdbsum/2psg PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2psg RCSB]</span> | ||
}} | }} | ||
| Line 23: | Line 26: | ||
[[Category: James, M N.G.]] | [[Category: James, M N.G.]] | ||
[[Category: Sielecki, A R.]] | [[Category: Sielecki, A R.]] | ||
| - | [[Category: PO3]] | ||
[[Category: hydrolase(acid proteinase zymogen)]] | [[Category: hydrolase(acid proteinase zymogen)]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:40:05 2008'' |
Revision as of 01:40, 31 March 2008
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| , resolution 1.8Å | |||||||
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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]. 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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