Substrate-induced double sided H-bond network as a means of domain closure in 3-phosphoglycerate kinase
Closure of the two domains of 3-phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot provide sufficient information about the mechanism of substrate assisted domain closure and about the requirement of only one or both substra...
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| Published in | FEBS letters Vol. 580; no. 11; pp. 2698 - 2706 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
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Elsevier B.V
15.05.2006
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| Abstract | Closure of the two domains of 3-phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot provide sufficient information about the mechanism of substrate assisted domain closure and about the requirement of only one or both substrates, since lattice forces may hinder the large scale domain movements. In this study the known X-ray data, obtained for the open and closed conformations, were probed by solution small-angle X-ray scattering experiments. The results prove that binding of both substrates is essential for domain closure. Molecular graphical analysis, indeed, reveals formation of a double-sided H-bond network, which affects substantially the shape of the main molecular hinge at β-strand L, under the concerted action of both substrates. |
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| AbstractList | Closure of the two domains of 3‐phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot provide sufficient information about the mechanism of substrate assisted domain closure and about the requirement of only one or both substrates, since lattice forces may hinder the large scale domain movements. In this study the known X‐ray data, obtained for the open and closed conformations, were probed by solution small‐angle X‐ray scattering experiments. The results prove that binding of both substrates is essential for domain closure. Molecular graphical analysis, indeed, reveals formation of a double‐sided H‐bond network, which affects substantially the shape of the main molecular hinge at β‐strand L, under the concerted action of both substrates. Closure of the two domains of 3-phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot provide sufficient information about the mechanism of substrate assisted domain closure and about the requirement of only one or both substrates, since lattice forces may hinder the large scale domain movements. In this study the known X-ray data, obtained for the open and closed conformations, were probed by solution small-angle X-ray scattering experiments. The results prove that binding of both substrates is essential for domain closure. Molecular graphical analysis, indeed, reveals formation of a double-sided H-bond network, which affects substantially the shape of the main molecular hinge at beta-strand L, under the concerted action of both substrates. |
| Author | Svergun, Dmitri Varga, Andrea Konarev, Peter Szabó, Judit Vas, Mária Flachner, Beáta Gráczer, Éva Závodszky, Péter |
| Author_xml | – sequence: 1 givenname: Andrea surname: Varga fullname: Varga, Andrea organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary – sequence: 2 givenname: Beáta surname: Flachner fullname: Flachner, Beáta organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary – sequence: 3 givenname: Peter surname: Konarev fullname: Konarev, Peter organization: EMBL Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany – sequence: 4 givenname: Éva surname: Gráczer fullname: Gráczer, Éva organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary – sequence: 5 givenname: Judit surname: Szabó fullname: Szabó, Judit organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary – sequence: 6 givenname: Dmitri surname: Svergun fullname: Svergun, Dmitri email: svergun@embl-hamburg.de organization: EMBL Outstation, c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany – sequence: 7 givenname: Péter surname: Závodszky fullname: Závodszky, Péter organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary – sequence: 8 givenname: Mária surname: Vas fullname: Vas, Mária email: vas@enzim.hu organization: Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1518 Budapest, P.O. Box 7, Hungary |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/16647059$$D View this record in MEDLINE/PubMed |
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| Copyright | 2006 Federation of European Biochemical Societies FEBS Letters 580 (2006) 1873-3468 © 2015 Federation of European Biochemical Societies |
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| Keywords | AMP-PCP PGK 3-PG Main hinge Domain movement Phosphoglycerate kinase ATP 1,3-BPG AMP-PNP Substrate effects SAXS Small-angle X-ray scattering |
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| Snippet | Closure of the two domains of 3-phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot... Closure of the two domains of 3‐phosphoglycerate kinase, upon substrate binding, is essential for the enzyme function. The available crystal structures cannot... |
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| SubjectTerms | 1,3-bisphosphoglycerate 1,3-BPG 3-PG 3-phospho-d-glycerate 3-phospho-d-glycerate 1-phosphotransferase (EC 2.7.2.3) 3-phospho-d-glycerate kinase AMP-PCP AMP-PNP ATP Domain movement Glyceric Acids - chemistry Glyceric Acids - metabolism Humans Hydrogen Bonding Main hinge Models, Molecular PGK Phosphoglycerate kinase Phosphoglycerate Kinase - chemistry Phosphoglycerate Kinase - metabolism Protein Structure, Tertiary SAXS Small-angle X-ray scattering Substrate effects Substrate Specificity β,γ-imido-adenosine-5′-triphosphate β,γ-methylene-adenosine-5′-triphosphate |
| Title | Substrate-induced double sided H-bond network as a means of domain closure in 3-phosphoglycerate kinase |
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