This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3ib0

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of C-lobe complex with diclofenac

Structural highlights

3ib0 is a 1 chain structure with sequence from Bos taurus. This structure supersedes the now removed PDB entries 2b6d and 3hwv. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.4Å
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

Nonsteroidal antiinflammatory drugs (NSAIDs), due to their good efficacy in the treatment of pain, inflammation, and fever, are among the most prescribed class of medicines in the world. The main drawback of NSAIDs is that they induce gastric complications such as peptic ulceration and injury to the intestine. Four NSAIDs, indomethacin, diclofenac, aspirin, and ibuprofen were selected to induce gastropathy in mouse models. It was found that the addition of C-terminal half of bovine lactoferrin (C-lobe) reversed the NSAID-induced injuries to the extent of 47-70% whereas the coadministration of C-lobe prevented it significantly. The C-lobe was prepared proteolytically using serine proteases. The binding studies of C-lobe with NSAIDs showed that these compounds bind to C-lobe with affinities ranging from 2.6 to 4.8 x 10(-4) M. The complexes of C-lobe were prepared with the above four NSAIDs. All four complexes were crystallized and their detailed three-dimensional structures were determined using x-ray crystallographic method. The structures showed that all the four NSAID molecules bound to C-lobe at the newly identified ligand binding site in C-lobe that is formed involving two alpha-helices, alpha10 and alpha11. The ligand binding site is separated from the well known iron binding site by the longest and the most stable beta-strand, betaj, in the structure. Similar results were also obtained with the full length lactoferrin molecule. This novel, to our knowledge, binding site in C-lobe of lactoferrin shows a good complementarity for the acidic and lipophilic compounds such as NSAIDs. We believe this indicates that C-lobe of lactoferrin can be exploited for the prevention of NSAID-induced gastropathy.

The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin.,Mir R, Singh N, Vikram G, Kumar RP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP Biophys J. 2009 Dec 16;97(12):3178-86. PMID:20006955^[9]

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

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ 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
↑ Mir R, Singh N, Vikram G, Kumar RP, Sinha M, Bhushan A, Kaur P, Srinivasan A, Sharma S, Singh TP. The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin. Biophys J. 2009 Dec 16;97(12):3178-86. PMID:20006955 doi:10.1016/j.bpj.2009.09.030

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ib0"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3ib0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2b6d 2b6d] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3hwv 3hwv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IB0 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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]] 1.4&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2b6d|2b6d]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=DIF:2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC+ACID'>DIF</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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=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'>[https://proteopedia.org/fgij/fg.htm?mol=3ib0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ib0 OCA], [https://pdbe.org/3ib0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ib0 RCSB], [https://www.ebi.ac.uk/pdbsum/3ib0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ib0 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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>
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 38: @@
 [[Category: Bos taurus]]
 [[Category: Large Structures]]
-[[Category: Kaur, P]]
+[[Category: Kaur P]]
-[[Category: Mir, R]]
+[[Category: Mir R]]
-[[Category: Sharma, S]]
+[[Category: Sharma S]]
-[[Category: Singh, N]]
+[[Category: Singh N]]
-[[Category: Singh, T P]]
+[[Category: Singh TP]]
-[[Category: Sinha, M]]
+[[Category: Sinha M]]
-[[Category: Srinivasan, A]]
+[[Category: Srinivasan A]]
-[[Category: Antibiotic]]
-[[Category: Antimicrobial]]
-[[Category: C-lobe]]
-[[Category: Disulfide bond]]
-[[Category: Drug]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Ion transport]]
-[[Category: Iron]]
-[[Category: Iron transport]]
-[[Category: Metal binding protein]]
-[[Category: Metal-binding]]
-[[Category: Phosphoprotein]]
-[[Category: Protease]]
-[[Category: Secreted]]
-[[Category: Serine protease]]
-[[Category: Transport]]

3ib0

From Proteopedia

Current revision

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of C-lobe complex with diclofenac

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox