Short hydrogen bonds in the catalytic mechanism of serine proteases
The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and...
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Serbian Chemical Society
2008-01-01
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doaj-628ee041765246d6928f959f8cb5c39b2020-12-30T07:54:49ZengSerbian Chemical Society Journal of the Serbian Chemical Society0352-51391820-74212008-01-0173439340310.2298/JSC0804393L0352-51390804393LShort hydrogen bonds in the catalytic mechanism of serine proteasesLeskovac Vladimir0Trivić Svetlana1Peričin Draginja2Popović Mira3Kandrač Julijan4Tehnološki fakultet, Novi SadPrirodno-matematički fakultet, Novi SadPoljoprivredni fakultet, Novi SadPrirodno-matematički fakultet, Novi SadPoljoprivredni fakultet, Novi SadThe survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 Å long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 Å long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes.http://www.doiserbia.nb.rs/img/doi/0352-5139/2008/0352-51390804393L.pdftrypsinserine proteaseslow-barrier hydrogen bonds |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Leskovac Vladimir Trivić Svetlana Peričin Draginja Popović Mira Kandrač Julijan |
spellingShingle |
Leskovac Vladimir Trivić Svetlana Peričin Draginja Popović Mira Kandrač Julijan Short hydrogen bonds in the catalytic mechanism of serine proteases Journal of the Serbian Chemical Society trypsin serine proteases low-barrier hydrogen bonds |
author_facet |
Leskovac Vladimir Trivić Svetlana Peričin Draginja Popović Mira Kandrač Julijan |
author_sort |
Leskovac Vladimir |
title |
Short hydrogen bonds in the catalytic mechanism of serine proteases |
title_short |
Short hydrogen bonds in the catalytic mechanism of serine proteases |
title_full |
Short hydrogen bonds in the catalytic mechanism of serine proteases |
title_fullStr |
Short hydrogen bonds in the catalytic mechanism of serine proteases |
title_full_unstemmed |
Short hydrogen bonds in the catalytic mechanism of serine proteases |
title_sort |
short hydrogen bonds in the catalytic mechanism of serine proteases |
publisher |
Serbian Chemical Society |
series |
Journal of the Serbian Chemical Society |
issn |
0352-5139 1820-7421 |
publishDate |
2008-01-01 |
description |
The survey of crystallographic data from the Protein Data Bank for 37 structures of trypsin and other serine proteases at a resolution of 0.78-1.28 Å revealed the presence of hydrogen bonds in the active site of the enzymes, which are formed between the catalytic histidine and aspartate residues and are on average 2.7 Å long. This is the typical bond length for normal hydrogen bonds. The geometric properties of the hydrogen bonds in the active site indicate that the H atom is not centered between the heteroatoms of the catalytic histidine and aspartate residues in the active site. Taken together, these findings exclude the possibility that short "low-barrier" hydrogen bonds are formed in the ground state structure of the active sites examined in this work. Some time ago, it was suggested by Cleland that the "low-barrier hydrogen bond" hypothesis is operative in the catalytic mechanism of serine proteases, and requires the presence of short hydrogen bonds around 2.4 Å long in the active site, with the H atom centered between the catalytic heteroatoms. The conclusions drawn from this work do not exclude the validity of the "low-barrier hydrogen bond" hypothesis at all, but they merely do not support it in this particular case, with this particular class of enzymes. |
topic |
trypsin serine proteases low-barrier hydrogen bonds |
url |
http://www.doiserbia.nb.rs/img/doi/0352-5139/2008/0352-51390804393L.pdf |
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