Sandbox Reserved 328: Difference between revisions
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{{STRUCTURE_1kar| PDB=1kar | SCENE= }} | {{STRUCTURE_1kar| PDB=1kar | SCENE= }} | ||
=L-Histidinol Dehydrogenase= | =L-Histidinol Dehydrogenase= | ||
Histidine biosynthesis consists of 10 enzymatic reactions, of which the last two are facilitated by the oxidoreductase l-histidinol-dehydrogenase (HisD). These consist of sequential NAD-dependent oxidations of l-histidinol to l-histidinaldehyde, follows by the similar conversion to l-histidine<ref name="1kar"> PMID:11842181 </ref>. | |||
==Overall Structure== | ==Overall Structure== | ||
HisD is a homodimer, with each subunit consisting of a globule segment, and an extending tail. The two larger domains (1 and 2) are within the globule, and domains 3 and 4 are found in the tail. The cores of both domains (residues 124–236 in domain 1 & 237–381 in domain 2) adopt incomplete Rossmann folds, which lack the last strand-helix hairpin<ref name="1kar" />. To carry out its function, HisD relies on the presence of one Zn2+ cation per monomer, not for catalysis, but for substrate binding. The Zn2+ cation is located at the bottom of the cavity occupied by the substrate and is octahedrally coordinated by four seperate residues. Along with Zn, the coordination of the substrate in the active site is assisted by the large degree of secondary structure present in the protein. The substrate binds in a deep pocket formed at the dimer interface between domains 1, 2, and 4, with most interactions being with residues at the N-terminal end of the β-sheet found within domain 2. Large amounts of secondary structure both in the form of <scene name='Sandbox_Reserved_328/Helices/1'>alpha helices</scene> and <scene name='Sandbox_Reserved_328/Beta_sheets/1'>beta sheets</scene> are present, and serve to provide a base for the overall structure of the molecule. | HisD is a homodimer, with each subunit consisting of a globule segment, and an extending tail. The two larger domains (1 and 2) are within the globule, and domains 3 and 4 are found in the tail. The cores of both domains (residues 124–236 in domain 1 & 237–381 in domain 2) adopt incomplete Rossmann folds, which lack the last strand-helix hairpin<ref name="1kar" />. To carry out its function, HisD relies on the presence of one Zn2+ cation per monomer, not for catalysis, but for substrate binding. The Zn2+ cation is located at the bottom of the cavity occupied by the substrate and is octahedrally coordinated by four seperate residues. Along with Zn, the coordination of the substrate in the active site is assisted by the large degree of secondary structure present in the protein. The substrate binds in a deep pocket formed at the dimer interface between domains 1, 2, and 4, with most interactions being with residues at the N-terminal end of the β-sheet found within domain 2. Large amounts of secondary structure both in the form of <scene name='Sandbox_Reserved_328/Helices/1'>alpha helices</scene> and <scene name='Sandbox_Reserved_328/Beta_sheets/1'>beta sheets</scene> are present, and serve to provide a base for the overall structure of the molecule. | ||
==Enzymatic mechanism== | ==Enzymatic mechanism== | ||
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The mechanism currently proposed by Teng and Grubmeyer<ref name="mech"> PMID:10353848 </ref> has been supported by structural data, and begins with the extraction of one proton and one hydride from L-histidinol<ref name="1kar" />. | The mechanism currently proposed by Teng and Grubmeyer<ref name="mech"> PMID:10353848 </ref> has been supported by structural data, and begins with the extraction of one proton and one hydride from L-histidinol<ref name="1kar" />. | ||
==Other information== | ==Other information== | ||
===Domain swapping=== | ===Domain swapping=== | ||
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===Domain Swapping=== | ===Domain Swapping=== | ||
Dimer formation most likely involves swapping of domains 3 and 4 between the two monomers, which explains the large amount of surface area (approximately 90%) buried upon dimerization. This type of domain swapping has been observed in other proteins as well<ref name="swap"> PMID:8580836 </ref>. | Dimer formation most likely involves swapping of domains 3 and 4 between the two monomers, which explains the large amount of surface area (approximately 90%) buried upon dimerization. This type of domain swapping has been observed in other proteins as well<ref name="swap"> PMID:8580836 </ref>. | ||
==References== | ==References== | ||
<references/> | <references/> | ||
Revision as of 21:25, 4 April 2011
| This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada. |
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| 1kar, resolution 2.10Å () | |||||||||
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| Ligands: | , | ||||||||
| Non-Standard Residues: | |||||||||
| Gene: | HISD (Escherichia coli) | ||||||||
| Activity: | Histidinol dehydrogenase, with EC number 1.1.1.23 | ||||||||
| Related: | 1k75, 1kae, 1kah | ||||||||
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| Resources: | FirstGlance, OCA, RCSB, PDBsum | ||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||
L-Histidinol DehydrogenaseL-Histidinol Dehydrogenase
Histidine biosynthesis consists of 10 enzymatic reactions, of which the last two are facilitated by the oxidoreductase l-histidinol-dehydrogenase (HisD). These consist of sequential NAD-dependent oxidations of l-histidinol to l-histidinaldehyde, follows by the similar conversion to l-histidine[1].
Overall StructureOverall Structure
HisD is a homodimer, with each subunit consisting of a globule segment, and an extending tail. The two larger domains (1 and 2) are within the globule, and domains 3 and 4 are found in the tail. The cores of both domains (residues 124–236 in domain 1 & 237–381 in domain 2) adopt incomplete Rossmann folds, which lack the last strand-helix hairpin[1]. To carry out its function, HisD relies on the presence of one Zn2+ cation per monomer, not for catalysis, but for substrate binding. The Zn2+ cation is located at the bottom of the cavity occupied by the substrate and is octahedrally coordinated by four seperate residues. Along with Zn, the coordination of the substrate in the active site is assisted by the large degree of secondary structure present in the protein. The substrate binds in a deep pocket formed at the dimer interface between domains 1, 2, and 4, with most interactions being with residues at the N-terminal end of the β-sheet found within domain 2. Large amounts of secondary structure both in the form of and are present, and serve to provide a base for the overall structure of the molecule.
Enzymatic mechanismEnzymatic mechanism
The mechanism currently proposed by Teng and Grubmeyer[2] has been supported by structural data, and begins with the extraction of one proton and one hydride from L-histidinol[1].
Other informationOther information
Domain swappingDomain swapping
Domains 1 and 2 show high similarity in their cores, in a structural way rather than having large amounts of residues in common[1]. This is also evident in the presense of hydrophobic residues forming the core of the domains.
Domain SwappingDomain Swapping
Dimer formation most likely involves swapping of domains 3 and 4 between the two monomers, which explains the large amount of surface area (approximately 90%) buried upon dimerization. This type of domain swapping has been observed in other proteins as well[3].
ReferencesReferences
- ↑ 1.0 1.1 1.2 1.3 Barbosa JA, Sivaraman J, Li Y, Larocque R, Matte A, Schrag JD, Cygler M. Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):1859-64. Epub 2002 Feb 12. PMID:11842181 doi:10.1073/pnas.022476199
- ↑ Teng H, Grubmeyer C. Mutagenesis of histidinol dehydrogenase reveals roles for conserved histidine residues. Biochemistry. 1999 Jun 1;38(22):7363-71. PMID:10353848 doi:10.1021/bi982758p
- ↑ Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 1995 Dec;4(12):2455-68. PMID:8580836 doi:http://dx.doi.org/10.1002/pro.5560041202