1bka
From Proteopedia
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|PDB= 1bka |SIZE=350|CAPTION= <scene name='initialview01'>1bka</scene>, resolution 2.4Å | |PDB= 1bka |SIZE=350|CAPTION= <scene name='initialview01'>1bka</scene>, resolution 2.4Å | ||
|SITE= <scene name='pdbsite=AN1:Oxalate+Binding+Site'>AN1</scene>, <scene name='pdbsite=AN2:Oxalate+Binding+Site'>AN2</scene>, <scene name='pdbsite=FE1:Fe+Binding+Site'>FE1</scene> and <scene name='pdbsite=FE2:Fe+Binding+Site'>FE2</scene> | |SITE= <scene name='pdbsite=AN1:Oxalate+Binding+Site'>AN1</scene>, <scene name='pdbsite=AN2:Oxalate+Binding+Site'>AN2</scene>, <scene name='pdbsite=FE1:Fe+Binding+Site'>FE1</scene> and <scene name='pdbsite=FE2:Fe+Binding+Site'>FE2</scene> | ||
| - | |LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene> | + | |LIGAND= <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=OXL:OXALATE+ION'>OXL</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bka OCA], [http://www.ebi.ac.uk/pdbsum/1bka PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bka RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations. | Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations. | ||
| - | |||
| - | ==Disease== | ||
| - | Known disease associated with this structure: Deafness, autosomal dominant 1 OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602121 602121]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Baker, H M.]] | [[Category: Baker, H M.]] | ||
[[Category: Smith, C A.]] | [[Category: Smith, C A.]] | ||
| - | [[Category: FE]] | ||
| - | [[Category: OXL]] | ||
[[Category: anion binding]] | [[Category: anion binding]] | ||
[[Category: iron binding protein]] | [[Category: iron binding protein]] | ||
| - | ''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 19:02:46 2008'' |
Revision as of 16:02, 30 March 2008
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| , resolution 2.4Å | |||||||
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| Sites: | , , and | ||||||
| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
OXALATE-SUBSTITUTED DIFERRIC LACTOFERRIN
Overview
Proteins of the transferrin family bind, with high affinity, two Fe3+ ions and two CO3(2)- ions but can also bind other metal ions and other anions. In order to find out how the protein structure and its two binding sites adapt to the binding of larger anions, we have determined the crystal structure of oxalate-substituted diferric lactoferrin at 2.4 A resolution. The final model has a crystallographic R-factor of 0.196 for all data in the range 8.0-2.4 A. Substitution of oxalate for carbonate does not produce any significant change in the polypeptide folding or domain closure. Both binding sites are perturbed, however, and the effects are different in each. In the C-lobe site the oxalate ion is bound to iron in symmetric 1,2-bidentate fashion whereas in the N-lobe the anion coordination is markedly asymmetric. The difference arises because in each site substitution of the larger anion causes displacement of the arginine that forms one wall of the anion binding site; the movement is different in each case, however, because of different interactions with "second shell" amino acid residues in the binding cleft. These observations provide an explanation for the site inequivalences that accompany the substitution of non-native anions and cations.
About this Structure
1BKA is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Anion binding by transferrins: importance of second-shell effects revealed by the crystal structure of oxalate-substituted diferric lactoferrin., Baker HM, Anderson BF, Brodie AM, Shongwe MS, Smith CA, Baker EN, Biochemistry. 1996 Jul 16;35(28):9007-13. PMID:8703903
Page seeded by OCA on Sun Mar 30 19:02:46 2008
