1nkx

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(New page: 200px<br /><applet load="1nkx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1nkx, resolution 1.90&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:1nkx.gif|left|200px]]<br /><applet load="1nkx" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1nkx, resolution 1.90&Aring;" />
 
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'''CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED FUNCTIONAL MONOFERRIC C-LOBE OF BOVINE LACTOFERRIN AT 1.9A RESOLUTION'''<br />
 
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==Overview==
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==CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED FUNCTIONAL MONOFERRIC C-LOBE OF BOVINE LACTOFERRIN AT 1.9A RESOLUTION==
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This is the first crystal structure of a proteolytically generated, functional C-lobe of lactoferrin. The purified samples of iron-saturated, C-lobe were crystallized in 0.1 M Mes buffer (pH 6.5) containing 25% (v/v), polyethyleneglycol monomethyl ether 550 M and 0.1 M zinc sulphate, heptahydrate. The X-ray intensity data were collected with 300 mm imaging, plate scanner mounted on a rotating anode generator. The structure was, determined by the molecular replacement method using the coordinates of, the C-terminal half of bovine lactoferrin as a search model and refined to, an R-factor of 0.193 for all data to 1.9A resolution. The final model, comprises 2593 protein atoms (residues 342-676 and 681-685), 124, carbohydrate atoms (from ten monosaccharide units, in three glycan, chains), one Fe(3+), one CO(3)(2-), two Zn(2+) and 230 water molecules., The overall folding of the C-lobe is essentially the same as that of, C-terminal half of bovine lactoferrin but differs slightly in, conformations of some of the loops and reveals a number of new, interactions. There are 20 Cys residues in the C-lobe forming ten, disulphide links. Out of these, one involving Cys481-Cys675 provides an, inter-domain link at 2.01A while another Cys405-Cys684 is formed between, the main C-lobe 342-676 and the hydrolyzed pentapeptide 681-685 fragment., Six inter-domain hydrogen bonds have been observed in the structure, whereas only four were reported in the structure of intact lactoferrin, although domain orientations have been found similar in the two, structures. The good quality of electron density has also revealed all the, ten oligosaccharide units in the structure. The observation of two metal, ions at sites other than the iron-binding cleft is another novel feature, of the present structure. These zinc ions stabilize the crystal packing., This structure is also notable for extensive inter-molecular hydrogen, bonding in the crystals. Therefore, the present structure appears to be, one of the best packed crystal structures among the proteins of the, transferrin superfamily.
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<StructureSection load='1nkx' size='340' side='right'caption='[[1nkx]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1nkx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKX FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkx OCA], [https://pdbe.org/1nkx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkx RCSB], [https://www.ebi.ac.uk/pdbsum/1nkx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TRFL_BOVIN TRFL_BOVIN] Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref> Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref> Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref> The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.<ref>PMID:8980754</ref> <ref>PMID:15222473</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nk/1nkx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1nkx ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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This is the first crystal structure of a proteolytically generated functional C-lobe of lactoferrin. The purified samples of iron-saturated C-lobe were crystallized in 0.1 M Mes buffer (pH 6.5) containing 25% (v/v) polyethyleneglycol monomethyl ether 550 M and 0.1 M zinc sulphate heptahydrate. The X-ray intensity data were collected with 300 mm imaging plate scanner mounted on a rotating anode generator. The structure was determined by the molecular replacement method using the coordinates of the C-terminal half of bovine lactoferrin as a search model and refined to an R-factor of 0.193 for all data to 1.9A resolution. The final model comprises 2593 protein atoms (residues 342-676 and 681-685), 124 carbohydrate atoms (from ten monosaccharide units, in three glycan chains), one Fe(3+), one CO(3)(2-), two Zn(2+) and 230 water molecules. The overall folding of the C-lobe is essentially the same as that of C-terminal half of bovine lactoferrin but differs slightly in conformations of some of the loops and reveals a number of new interactions. There are 20 Cys residues in the C-lobe forming ten disulphide links. Out of these, one involving Cys481-Cys675 provides an inter-domain link at 2.01A while another Cys405-Cys684 is formed between the main C-lobe 342-676 and the hydrolyzed pentapeptide 681-685 fragment. Six inter-domain hydrogen bonds have been observed in the structure whereas only four were reported in the structure of intact lactoferrin, although domain orientations have been found similar in the two structures. The good quality of electron density has also revealed all the ten oligosaccharide units in the structure. The observation of two metal ions at sites other than the iron-binding cleft is another novel feature of the present structure. These zinc ions stabilize the crystal packing. This structure is also notable for extensive inter-molecular hydrogen bonding in the crystals. Therefore, the present structure appears to be one of the best packed crystal structures among the proteins of the transferrin superfamily.
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==About this Structure==
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Crystal structure of a proteolytically generated functional monoferric C-lobe of bovine lactoferrin at 1.9A resolution.,Sharma S, Jasti J, Kumar J, Mohanty AK, Singh TP J Mol Biol. 2003 Aug 8;331(2):485-96. PMID:12888354<ref>PMID:12888354</ref>
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1NKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with NAG, FE, ZN and CO3 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NKX OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystal structure of a proteolytically generated functional monoferric C-lobe of bovine lactoferrin at 1.9A resolution., Sharma S, Jasti J, Kumar J, Mohanty AK, Singh TP, J Mol Biol. 2003 Aug 8;331(2):485-96. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12888354 12888354]
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</div>
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[[Category: Bos taurus]]
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<div class="pdbe-citations 1nkx" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Jasti, J.]]
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[[Category: Kumar, J.]]
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[[Category: Mohanty, A.K.]]
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[[Category: Sharma, S.]]
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[[Category: Singh, T.P.]]
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[[Category: CO3]]
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[[Category: FE]]
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[[Category: NAG]]
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[[Category: ZN]]
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[[Category: c-lobe]]
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[[Category: fragment]]
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[[Category: lactoferrin]]
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[[Category: trypsin]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:21:02 2007''
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==See Also==
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*[[Lactoferrin|Lactoferrin]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bos taurus]]
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[[Category: Large Structures]]
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[[Category: Jasti J]]
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[[Category: Kumar J]]
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[[Category: Mohanty AK]]
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[[Category: Sharma S]]
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[[Category: Singh TP]]

Current revision

CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED FUNCTIONAL MONOFERRIC C-LOBE OF BOVINE LACTOFERRIN AT 1.9A RESOLUTION

PDB ID 1nkx

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