Cargando…
Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP
The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia su...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659122/ https://www.ncbi.nlm.nih.gov/pubmed/23700444 http://dx.doi.org/10.1371/journal.pone.0064004 |
_version_ | 1782270407899873280 |
---|---|
author | Lim, Kap Kulakova, Liudmila Galkin, Andrey Herzberg, Osnat |
author_facet | Lim, Kap Kulakova, Liudmila Galkin, Andrey Herzberg, Osnat |
author_sort | Lim, Kap |
collection | PubMed |
description | The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK) with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP), was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123–170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent. |
format | Online Article Text |
id | pubmed-3659122 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-36591222013-05-22 Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP Lim, Kap Kulakova, Liudmila Galkin, Andrey Herzberg, Osnat PLoS One Research Article The parasite Giardia lamblia utilizes the L-arginine dihydrolase pathway to generate ATP from L-arginine. Carbamate kinase (CK) catalyzes the last step in this pathway, converting ADP and carbamoyl phosphate to ATP and ammonium carbamate. Because the L-arginine pathway is essential for G. lamblia survival and absent in high eukaryotes including humans, the enzyme is a potential target for drug development. We have determined two crystal structures of G. lamblia CK (glCK) with bound ligands. One structure, in complex with a nonhydrolyzable ATP analog, adenosine 5′-adenylyl-β,γ-imidodiphosphate (AMP-PNP), was determined at 2.6 Å resolution. The second structure, in complex with citric acid bound in the postulated carbamoyl phosphate binding site, was determined in two slightly different states at 2.1 and 2.4 Å resolution. These structures reveal conformational flexibility of an auxiliary domain (amino acid residues 123–170), which exhibits open or closed conformations or structural disorder, depending on the bound ligand. The structures also reveal a smaller conformational change in a region associated the AMP-PNP adenine binding site. The protein residues involved in binding, together with a model of the transition state, suggest that catalysis follows an in-line, predominantly dissociative, phosphotransfer reaction mechanism, and that closure of the flexible auxiliary domain is required to protect the transition state from bulk solvent. Public Library of Science 2013-05-20 /pmc/articles/PMC3659122/ /pubmed/23700444 http://dx.doi.org/10.1371/journal.pone.0064004 Text en © 2013 Lim et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Lim, Kap Kulakova, Liudmila Galkin, Andrey Herzberg, Osnat Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title | Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title_full | Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title_fullStr | Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title_full_unstemmed | Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title_short | Crystal Structures of Carbamate Kinase from Giardia lamblia Bound with Citric Acid and AMP-PNP |
title_sort | crystal structures of carbamate kinase from giardia lamblia bound with citric acid and amp-pnp |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3659122/ https://www.ncbi.nlm.nih.gov/pubmed/23700444 http://dx.doi.org/10.1371/journal.pone.0064004 |
work_keys_str_mv | AT limkap crystalstructuresofcarbamatekinasefromgiardialambliaboundwithcitricacidandamppnp AT kulakovaliudmila crystalstructuresofcarbamatekinasefromgiardialambliaboundwithcitricacidandamppnp AT galkinandrey crystalstructuresofcarbamatekinasefromgiardialambliaboundwithcitricacidandamppnp AT herzbergosnat crystalstructuresofcarbamatekinasefromgiardialambliaboundwithcitricacidandamppnp |