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| - | [[Image:4fgf.jpg|left|200px]]<br /><applet load="4fgf" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="4fgf, resolution 1.6Å" /> | |
| - | '''REFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION AND ANALYSIS OF PRESUMED HEPARIN BINDING SITES BY SELENATE SUBSTITUTION'''<br /> | |
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| - | ==Overview== | + | ==REFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION AND ANALYSIS OF PRESUMED HEPARIN BINDING SITES BY SELENATE SUBSTITUTION== |
| - | The three-dimensional structure of human basic fibroblast growth factor, has been refined to a crystallographic residual of 16.1% at 1.6 A, resolution. The structure has a Kunitz-type fold and is composed of 12, antiparallel beta-strands, 6 of which form a beta-barrel. One bound, sulfate ion has been identified in the model, hydrogen bonded to the side, chains of Asn 27, Arg 120, and Lys 125. The side chain of Arg 120 has two, conformations, both of which permit hydrogen bonds to the sulfate. This, sulfate binding site has been suggested as the binding site for heparin, (Eriksson, A.E., Cousens, L.S., Weaver, L.H., & Matthews, B.W., 1991, Proc. Natl. Acad. Sci. USA 88, 3441-3445). Two beta-mercaptoethanol (BME), molecules are also included in the model, each forming a disulfide bond to, the S gamma atoms of Cys 69 and Cys 92, respectively. The side chain of, Cys 92 has two conformations of which only one can bind BME. Therefore the, BME molecule is half occupied at this site. The locations of possible, sulfate binding sites on the protein were examined by replacing the, ammonium sulfate in the crystallization medium with ammonium selenate., Diffraction data were measured to 2.2 A resolution and the structure, refined to an R-factor of 13.8%. The binding of the more electron-dense, selenate ion was identified at two positions. One position was identical, to the sulfate binding site identified previously. The second selenate, binding site, which is of lower occupancy, is situated 5.6 A from the, first. This ion is hydrogen bonded by the side chain of Lys 135 and Arg, 120. Thus the side chain of Arg 120 binds two selenate ions, simultaneously. It is suggested that the observed second selenate binding, site should also be considered as a possible binding site for heparin, or, that both selenate binding sites might simultaneously contribute to the, binding of heparin. | + | <StructureSection load='4fgf' size='340' side='right'caption='[[4fgf]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[4fgf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FGF FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4fgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fgf OCA], [https://pdbe.org/4fgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fgf RCSB], [https://www.ebi.ac.uk/pdbsum/4fgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fgf ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/FGF2_HUMAN FGF2_HUMAN] Plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation and cell migration. Functions as potent mitogen in vitro.<ref>PMID:1721615</ref> <ref>PMID:8663044</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fg/4fgf_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=4fgf ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | The three-dimensional structure of human basic fibroblast growth factor has been refined to a crystallographic residual of 16.1% at 1.6 A resolution. The structure has a Kunitz-type fold and is composed of 12 antiparallel beta-strands, 6 of which form a beta-barrel. One bound sulfate ion has been identified in the model, hydrogen bonded to the side chains of Asn 27, Arg 120, and Lys 125. The side chain of Arg 120 has two conformations, both of which permit hydrogen bonds to the sulfate. This sulfate binding site has been suggested as the binding site for heparin (Eriksson, A.E., Cousens, L.S., Weaver, L.H., & Matthews, B.W., 1991, Proc. Natl. Acad. Sci. USA 88, 3441-3445). Two beta-mercaptoethanol (BME) molecules are also included in the model, each forming a disulfide bond to the S gamma atoms of Cys 69 and Cys 92, respectively. The side chain of Cys 92 has two conformations of which only one can bind BME. Therefore the BME molecule is half occupied at this site. The locations of possible sulfate binding sites on the protein were examined by replacing the ammonium sulfate in the crystallization medium with ammonium selenate. Diffraction data were measured to 2.2 A resolution and the structure refined to an R-factor of 13.8%. The binding of the more electron-dense selenate ion was identified at two positions. One position was identical to the sulfate binding site identified previously. The second selenate binding site, which is of lower occupancy, is situated 5.6 A from the first. This ion is hydrogen bonded by the side chain of Lys 135 and Arg 120. Thus the side chain of Arg 120 binds two selenate ions simultaneously. It is suggested that the observed second selenate binding site should also be considered as a possible binding site for heparin, or that both selenate binding sites might simultaneously contribute to the binding of heparin. |
| | | | |
| - | ==Disease==
| + | Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.,Eriksson AE, Cousens LS, Matthews BW Protein Sci. 1993 Aug;2(8):1274-84. PMID:7691311<ref>PMID:7691311</ref> |
| - | Known diseases associated with this structure: Hypophosphatemic rickets, autosomal dominant OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=605380 605380]], Osteomalacia, tumor-induced OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=605380 605380]], Tumoral calcinosis, hyperphosphatemic, familial OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=605380 605380]]
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 4FGF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=BME:'>BME</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 3FGF. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FGF OCA].
| + | </div> |
| | + | <div class="pdbe-citations 4fgf" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution., Eriksson AE, Cousens LS, Matthews BW, Protein Sci. 1993 Aug;2(8):1274-84. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7691311 7691311]
| + | *[[Fibroblast growth factor 3D structures|Fibroblast growth factor 3D structures]] |
| | + | == References == |
| | + | <references/> |
| | + | __TOC__ |
| | + | </StructureSection> |
| | [[Category: Homo sapiens]] | | [[Category: Homo sapiens]] |
| - | [[Category: Single protein]] | + | [[Category: Large Structures]] |
| - | [[Category: Eriksson, A.E.]] | + | [[Category: Eriksson AE]] |
| - | [[Category: Matthews, B.W.]] | + | [[Category: Matthews BW]] |
| - | [[Category: BME]]
| + | |
| - | [[Category: SO4]]
| + | |
| - | [[Category: growth factor]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:44:47 2008''
| + | |
| Structural highlights
Function
FGF2_HUMAN Plays an important role in the regulation of cell survival, cell division, angiogenesis, cell differentiation and cell migration. Functions as potent mitogen in vitro.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The three-dimensional structure of human basic fibroblast growth factor has been refined to a crystallographic residual of 16.1% at 1.6 A resolution. The structure has a Kunitz-type fold and is composed of 12 antiparallel beta-strands, 6 of which form a beta-barrel. One bound sulfate ion has been identified in the model, hydrogen bonded to the side chains of Asn 27, Arg 120, and Lys 125. The side chain of Arg 120 has two conformations, both of which permit hydrogen bonds to the sulfate. This sulfate binding site has been suggested as the binding site for heparin (Eriksson, A.E., Cousens, L.S., Weaver, L.H., & Matthews, B.W., 1991, Proc. Natl. Acad. Sci. USA 88, 3441-3445). Two beta-mercaptoethanol (BME) molecules are also included in the model, each forming a disulfide bond to the S gamma atoms of Cys 69 and Cys 92, respectively. The side chain of Cys 92 has two conformations of which only one can bind BME. Therefore the BME molecule is half occupied at this site. The locations of possible sulfate binding sites on the protein were examined by replacing the ammonium sulfate in the crystallization medium with ammonium selenate. Diffraction data were measured to 2.2 A resolution and the structure refined to an R-factor of 13.8%. The binding of the more electron-dense selenate ion was identified at two positions. One position was identical to the sulfate binding site identified previously. The second selenate binding site, which is of lower occupancy, is situated 5.6 A from the first. This ion is hydrogen bonded by the side chain of Lys 135 and Arg 120. Thus the side chain of Arg 120 binds two selenate ions simultaneously. It is suggested that the observed second selenate binding site should also be considered as a possible binding site for heparin, or that both selenate binding sites might simultaneously contribute to the binding of heparin.
Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.,Eriksson AE, Cousens LS, Matthews BW Protein Sci. 1993 Aug;2(8):1274-84. PMID:7691311[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Shimoyama Y, Gotoh M, Ino Y, Sakamoto M, Kato K, Hirohashi S. Characterization of high-molecular-mass forms of basic fibroblast growth factor produced by hepatocellular carcinoma cells: possible involvement of basic fibroblast growth factor in hepatocarcinogenesis. Jpn J Cancer Res. 1991 Nov;82(11):1263-70. PMID:1721615
- ↑ Ornitz DM, Xu J, Colvin JS, McEwen DG, MacArthur CA, Coulier F, Gao G, Goldfarb M. Receptor specificity of the fibroblast growth factor family. J Biol Chem. 1996 Jun 21;271(25):15292-7. PMID:8663044
- ↑ Eriksson AE, Cousens LS, Matthews BW. Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution. Protein Sci. 1993 Aug;2(8):1274-84. PMID:7691311
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