2d0w
From Proteopedia
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|PDB= 2d0w |SIZE=350|CAPTION= <scene name='initialview01'>2d0w</scene>, resolution 1.98Å | |PDB= 2d0w |SIZE=350|CAPTION= <scene name='initialview01'>2d0w</scene>, resolution 1.98Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[2d0v|2D0V]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d0w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d0w OCA], [http://www.ebi.ac.uk/pdbsum/2d0w PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d0w RCSB]</span> | ||
}} | }} | ||
| Line 26: | Line 29: | ||
[[Category: Suzuki, S.]] | [[Category: Suzuki, S.]] | ||
[[Category: Yamaguchi, K.]] | [[Category: Yamaguchi, K.]] | ||
| - | [[Category: HEM]] | ||
| - | [[Category: ZN]] | ||
[[Category: cytochrome]] | [[Category: cytochrome]] | ||
[[Category: electron transfer]] | [[Category: electron transfer]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:29:00 2008'' |
Revision as of 23:29, 30 March 2008
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| , resolution 1.98Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Related: | 2D0V
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of cytochrome cL from Hyphomicrobium denitrificans
Overview
Methanol dehydrogenase (Hd-MDH) and its physiological electron acceptor, cytochrome c(L) (Hd-Cyt c(L)), isolated from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans A3151, have been kinetically and structurally characterized; the X-ray structures of Hd-MDH and Hd-Cyt c(L) have been determined using molecular replacement at 2.5 and 2.0 A resolution, respectively. To explain the mechanism for electron transfer between these proteins, the dependence of MDH activity on the concentration of Hd-Cyt c(L) has been investigated at pH 4.5-7.0. The Michaelis constant for Hd-Cyt c(L) shows the smallest value (approximately 0.3 microM) at pH 5.5. The pseudo-first-order rate constant (k(obs)) of the reduction of Hd-Cyt c(L) exhibits a hyperbolic concentration dependence of Hd-MDH at pH 5.5, although k(obs) linearly increases at pH 6.5. These findings indicate formation of a transient complex between these proteins during an electron transfer event. Hd-MDH (148 kDa) is a large tetrameric protein with an alpha(2)beta(2) subunit composition, showing a high degree of structural similarity with other MDHs. Hd-Cyt c(L) (19 kDa) exhibiting the alpha-band at 550.7 nm has a unique C-terminal region involving a disulfide bond between Cys47 and Cys165. Moreover, there is a pair of Hd-Cyt c(L) monomers related with a pseudo-2-fold axis of symmetry in the asymmetric unit, and the two monomers tightly interact with each other through three hydrogen bonds. This configuration is the first example in the studies of cytochrome c as the physiological electron acceptor for MDH. The docking simulation between the coupled Hd-Cyt c(L) molecules and the heterotetrameric Hd-MDH molecule has been carried out.
About this Structure
2D0W is a Single protein structure of sequence from Hyphomicrobium denitrificans. Full crystallographic information is available from OCA.
Reference
Crystal structures of cytochrome c(L) and methanol dehydrogenase from Hyphomicrobium denitrificans: structural and mechanistic insights into interactions between the two proteins., Nojiri M, Hira D, Yamaguchi K, Okajima T, Tanizawa K, Suzuki S, Biochemistry. 2006 Mar 21;45(11):3481-92. PMID:16533029
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