1m1y
From Proteopedia
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|PDB= 1m1y |SIZE=350|CAPTION= <scene name='initialview01'>1m1y</scene>, resolution 3.2Å | |PDB= 1m1y |SIZE=350|CAPTION= <scene name='initialview01'>1m1y</scene>, resolution 3.2Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CFM:FE-MO-S+CLUSTER'>CFM</scene>, <scene name='pdbligand=CLF:FE(8)-S(7)+CLUSTER'>CLF</scene>, <scene name='pdbligand=HCA:3-HYDROXY-3-CARBOXY-ADIPIC+ACID'>HCA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrogenase Nitrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.18.6.1 1.18.6.1] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1n2c|1n2c]], [[3min|3min]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m1y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m1y OCA], [http://www.ebi.ac.uk/pdbsum/1m1y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1m1y RCSB]</span> | ||
}} | }} | ||
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[[Category: Willing, A.]] | [[Category: Willing, A.]] | ||
[[Category: Yoshida, M.]] | [[Category: Yoshida, M.]] | ||
| - | [[Category: CA]] | ||
| - | [[Category: CFM]] | ||
| - | [[Category: CLF]] | ||
| - | [[Category: HCA]] | ||
| - | [[Category: SF4]] | ||
[[Category: chemical crosslink]] | [[Category: chemical crosslink]] | ||
[[Category: nitrogen fixation]] | [[Category: nitrogen fixation]] | ||
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[[Category: protein interaction]] | [[Category: protein interaction]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:10:20 2008'' |
Revision as of 19:10, 30 March 2008
| |||||||
| , resolution 3.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Activity: | Nitrogenase, with EC number 1.18.6.1 | ||||||
| Related: | 1n2c, 3min
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Chemical Crosslink of Nitrogenase MoFe Protein and Fe Protein
Overview
The transient formation of a complex between the component Fe- and MoFe-proteins of nitrogenase represents a central event in the substrate reduction mechanism of this enzyme. Previously, we have isolated an N-[3-(dimethylamino)propyl]-N'-ethylcarbodiimide (EDC) cross-linked complex of these proteins stabilized by a covalent isopeptide linkage between Glu 112 and Lys beta400 of the Fe-protein and MoFe-protein, respectively [Willing, A., et al. (1989) J. Biol. Chem. 264, 8499-8503; Willing, A., and Howard, J. B. (1990) J. Biol. Chem. 265, 6596-6599]. We report here the biochemical and structural characterization of the cross-linked complex to assess the mechanistic relevance of this species. Glycinamide inhibits the cross-linking reaction, and is found to be specifically incorporated into Glu 112 of the Fe-protein, without detectable modification of either of the neighboring residues (Glu 110 and Glu 111). This modified protein is still competent for substrate reduction, demonstrating that formation of the cross-linked complex is responsible for the enzymatic inactivation, and not the EDC reaction or the modification of the Fe-protein. Crystallographic analysis of the EDC-cross-linked complex at 3.2 A resolution confirms the site of the isopeptide linkage. The nature of the protein surfaces around the cross-linking site suggests there is a strong electrostatic component to the formation of the complex, although the interface area between the component proteins is small. The binding footprints between proteins in the cross-linked complex are adjacent, but with little overlap, to those observed in the complex of the nitrogenase proteins stabilized by ADP-AlF(4)(-). The results of these studies suggest that EDC cross-linking traps a nucleotide-independent precomplex of the nitrogenase proteins driven by complementary electrostatic interactions that subsequently rearranges in a nucleotide-dependent fashion to the electron transfer competent state observed in the ADP-AlF(4)(-) structure.
About this Structure
1M1Y is a Protein complex structure of sequences from Azotobacter vinelandii. Full crystallographic information is available from OCA.
Reference
Biochemical and structural characterization of the cross-linked complex of nitrogenase: comparison to the ADP-AlF4(-)-stabilized structure., Schmid B, Einsle O, Chiu HJ, Willing A, Yoshida M, Howard JB, Rees DC, Biochemistry. 2002 Dec 31;41(52):15557-65. PMID:12501184
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