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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| Format: | Article |
| Language: | English |
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Serbian Chemical Society
2008-01-01
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| Series: | Journal of the Serbian Chemical Society |
| Subjects: | |
| Online Access: | http://www.doiserbia.nb.rs/img/doi/0352-5139/2008/0352-51390804393L.pdf |
| _version_ | 1819280542532632576 |
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| author | Leskovac Vladimir Trivić Svetlana Peričin Draginja Popović Mira Kandrač Julijan |
| author_facet | Leskovac Vladimir Trivić Svetlana Peričin Draginja Popović Mira Kandrač Julijan |
| author_sort | Leskovac Vladimir |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-24T00:45:27Z |
| format | Article |
| id | doaj.art-628ee041765246d6928f959f8cb5c39b |
| institution | Directory Open Access Journal |
| issn | 0352-5139 1820-7421 |
| language | English |
| last_indexed | 2024-12-24T00:45:27Z |
| publishDate | 2008-01-01 |
| publisher | Serbian Chemical Society |
| record_format | Article |
| series | Journal of the Serbian Chemical Society |
| spelling | doaj.art-628ee041765246d6928f959f8cb5c39b2022-12-21T17:23:48ZengSerbian Chemical SocietyJournal 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 |
| 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 |
| title | 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_short | Short hydrogen bonds in the catalytic mechanism of serine proteases |
| title_sort | short hydrogen bonds in the catalytic mechanism of serine proteases |
| 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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