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...

Full description

Bibliographic Details
Main Authors: Leskovac Vladimir, Trivić Svetlana, Peričin Draginja, Popović Mira, Kandrač Julijan
Format: Article
Language:English
Published: Serbian Chemical Society 2008-01-01
Series:Journal of the Serbian Chemical Society
Subjects:
Online Access:http://www.doiserbia.nb.rs/img/doi/0352-5139/2008/0352-51390804393L.pdf
id doaj-628ee041765246d6928f959f8cb5c39b
record_format Article
spelling 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
work_keys_str_mv AT leskovacvladimir shorthydrogenbondsinthecatalyticmechanismofserineproteases
AT trivicsvetlana shorthydrogenbondsinthecatalyticmechanismofserineproteases
AT pericindraginja shorthydrogenbondsinthecatalyticmechanismofserineproteases
AT popovicmira shorthydrogenbondsinthecatalyticmechanismofserineproteases
AT kandracjulijan shorthydrogenbondsinthecatalyticmechanismofserineproteases
_version_ 1724365873441931264