3k0v: Difference between revisions

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==Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution==
==Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution==
<StructureSection load='3k0v' size='340' side='right' caption='[[3k0v]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
<StructureSection load='3k0v' size='340' side='right'caption='[[3k0v]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3k0v]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K0V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K0V FirstGlance]. <br>
<table><tr><td colspan='2'>[[3k0v]] 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=3K0V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K0V FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=DXI:BETA-D-GLUCOPYRANOSYL-(1- 4)-BETA-D-GALACTOPYRANOSYL-(1- 4)-ALPHA-D-GLUCOPYRANOSE'>DXI</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.91&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2dwa|2dwa]], [[2dxy|2dxy]], [[3ibo|3ibo]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k0v OCA], [http://pdbe.org/3k0v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k0v RCSB], [http://www.ebi.ac.uk/pdbsum/3k0v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k0v ProSAT]</span></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=3k0v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k0v OCA], [https://pdbe.org/3k0v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k0v RCSB], [https://www.ebi.ac.uk/pdbsum/3k0v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k0v ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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>
[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>  
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/3k0v_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/3k0v_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </jmolCheckbox>
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</StructureSection>
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Kaur, P]]
[[Category: Large Structures]]
[[Category: Mir, R]]
[[Category: Kaur P]]
[[Category: Sharma, S]]
[[Category: Mir R]]
[[Category: Singh, N]]
[[Category: Sharma S]]
[[Category: Singh, T P]]
[[Category: Singh N]]
[[Category: Sinha, M]]
[[Category: Singh TP]]
[[Category: Vikram, G]]
[[Category: Sinha M]]
[[Category: Antibiotic]]
[[Category: Vikram G]]
[[Category: Antimicrobial]]
[[Category: C-lobe]]
[[Category: Complex]]
[[Category: Dextrin]]
[[Category: Disulfide bond]]
[[Category: Glycoprotein]]
[[Category: Hydrolase]]
[[Category: Ion transport]]
[[Category: Iron]]
[[Category: Iron transport]]
[[Category: Metal-binding]]
[[Category: Phosphoprotein]]
[[Category: Protease]]
[[Category: Secreted]]
[[Category: Serine protease]]
[[Category: Transport]]

Latest revision as of 09:23, 27 November 2024

Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolutionRemoval of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution

Structural highlights

3k0v is a 1 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.91Å
Ligands:, , , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.[1] [2] Lactotransferrin has antimicrobial activity. The most effective inhibitory activity was seen against E.coli and P.aeruginosa.[3] [4] Lactoferricin B is an antimicrobial peptide. Inhibits the growth of Gram-negative and Gram-positive bacteria.[5] [6] 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.[7] [8]

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

Bovine lactoferrin has been shown to reduce the levels of glucose in both normal subjects and non-insulin dependent diabetic patients. The binding studies have shown that various sugar molecules interact with lactoferrin indicating the presence of a sugar-binding site in the protein. Structural studies have revealed that the sugar-binding site is located in the C-terminal half (C-lobe) of bilobal lactoferrin. Since the sugar-binding site was part of the C-lobe, it was better to carry out binding and structural studies using C-lobe rather than the full protein molecule. Therefore, C-lobe was prepared by limited proteolysis of lactoferrin with enzyme proteinase K. It was purified to homogeneity for further studies. The addition of C-lobe to human serum showed significant lowering of glucose levels. The binding studies using C-lobe with nine sugars, glucose, galactose, mannose, xylose, maltose, cellobiose, lactose, sucrose and dextrin gave values of binding constants in the range of 10(-4) to 10(-5)M. The structure determinations of the complexes of C-lobe with all the nine sugars showed that all of them interact with C-lobe through the same recognition site involving several hydrogen bonds and van der Waals interactions.

Specific interactions of C-terminal half (C-lobe) of lactoferrin protein with edible sugars: binding and structural studies with implications on diabetes.,Mir R, Kumar RP, Singh N, Vikram GP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP Int J Biol Macromol. 2010 Jul 1;47(1):50-9. Epub 2010 Apr 4. PMID:20371371[9]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
  2. ↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
  3. ↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
  4. ↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
  5. ↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
  6. ↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
  7. ↑ Hoek KS, Milne JM, Grieve PA, Dionysius DA, Smith R. Antibacterial activity in bovine lactoferrin-derived peptides. Antimicrob Agents Chemother. 1997 Jan;41(1):54-9. PMID:8980754
  8. ↑ Massucci MT, Giansanti F, Di Nino G, Turacchio M, Giardi MF, Botti D, Ippoliti R, De Giulio B, Siciliano RA, Donnarumma G, Valenti P, Bocedi A, Polticelli F, Ascenzi P, Antonini G. Proteolytic activity of bovine lactoferrin. Biometals. 2004 Jun;17(3):249-55. PMID:15222473
  9. ↑ Mir R, Kumar RP, Singh N, Vikram GP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP. Specific interactions of C-terminal half (C-lobe) of lactoferrin protein with edible sugars: binding and structural studies with implications on diabetes. Int J Biol Macromol. 2010 Jul 1;47(1):50-9. Epub 2010 Apr 4. PMID:20371371 doi:10.1016/j.ijbiomac.2010.03.021

3k0v, resolution 1.91Å

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