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(-) Description

Title :  FRAGMENT BASED APPROACH AND BINDING BEHAVIOR OF LFAMPINB WITH LIPOPOLYSACCHARIDE: BIOPHYSICAL ASPECTS
 
Authors :  A. Bhunia, S. Chatterjee, A. Ghosh, J. Jana
Date :  29 Aug 13  (Deposition) - 25 Sep 13  (Release) - 02 Sep 15  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
NMR Structure *:  A  (1x)
Keywords :  Antimicrobial Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ghosh, A. Datta, J. Jana, R. K. Kar, C. Chatterjee, S. Chatterjee, A. Bhunia
Sequence Context Induced Antimicrobial Activity: Insight Into Lipopolysaccharide Permeabilization.
Mol Biosyst V. 10 1596 2014
PubMed-ID: 24714742  |  Reference-DOI: 10.1039/C4MB00111G

(-) Compounds

Molecule 1 - LACTOTRANSFERRIN
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Organism CommonBOVINE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    SynonymLACTOFERRIN, LACTOFERRICIN-B, LFCIN-B
    SyntheticYES

 Structural Features

(-) Chains, Units

  1
NMR Structure (10x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2MD4)

(-) Sites  (0, 0)

(no "Site" information available for 2MD4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MD4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MD4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MD4)

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000017041ENSBTAE00000406255chr22:54313830-54314011182TRFL_BOVIN1-15150--
1.2ENSBTAT000000017042ENSBTAE00000391946chr22:54317754-54317917164TRFL_BOVIN15-69550--
1.3ENSBTAT000000017043ENSBTAE00000378931chr22:54320894-54321002109TRFL_BOVIN70-106370--
1.4ENSBTAT000000017044ENSBTAE00000247433chr22:54321299-54321481183TRFL_BOVIN106-167620--
1.5ENSBTAT000000017045ENSBTAE00000013647chr22:54322098-54322245148TRFL_BOVIN167-216500--
1.6ENSBTAT000000017046ENSBTAE00000247432chr22:54323189-5432324456TRFL_BOVIN216-235200--
1.7ENSBTAT000000017047ENSBTAE00000013649chr22:54328592-54328770179TRFL_BOVIN235-294601A:1-88
1.8ENSBTAT000000017048ENSBTAE00000013654chr22:54329198-54329372175TRFL_BOVIN295-353591A:9-124
1.9ENSBTAT000000017049ENSBTAE00000013658chr22:54329898-54330052155TRFL_BOVIN353-404520--
1.10ENSBTAT0000000170410ENSBTAE00000013661chr22:54332009-5433209991TRFL_BOVIN405-435310--
1.11ENSBTAT0000000170411ENSBTAE00000013664chr22:54334326-5433437348TRFL_BOVIN435-451170--
1.12ENSBTAT0000000170412ENSBTAE00000013668chr22:54334997-54335152156TRFL_BOVIN451-503530--
1.13ENSBTAT0000000170413ENSBTAE00000013670chr22:54337061-54337202142TRFL_BOVIN503-550480--
1.14ENSBTAT0000000170414ENSBTAE00000013674chr22:54341961-5434202868TRFL_BOVIN550-573240--
1.15ENSBTAT0000000170415ENSBTAE00000013678chr22:54343949-54344133185TRFL_BOVIN573-634620--
1.16ENSBTAT0000000170416ENSBTAE00000429733chr22:54345264-54345453190TRFL_BOVIN635-698640--
1.17ENSBTAT0000000170417ENSBTAE00000407091chr22:54347010-54347235226TRFL_BOVIN698-708110--

(-) Sequences/Alignments

NMR Structure
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:12
 aligned with TRFL_BOVIN | P24627 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:12
                                   296  
           TRFL_BOVIN   287 WKLLSKAQEKFG 298
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
               Transcript 1 Exon 1.71.8  Transcript 1
                 2md4 A   1 WKLLSKAQEKFG  12
                                    10  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2MD4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MD4)

(-) Gene Ontology  (50, 50)

NMR Structure(hide GO term definitions)
Chain A   (TRFL_BOVIN | P24627)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0019732    antifungal humoral response    An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
    GO:0060349    bone morphogenesis    The process in which bones are generated and organized.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0002227    innate immune response in mucosa    Any process of the innate immune response that takes place in the mucosal tissues.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0044793    negative regulation by host of viral process    A process in which a host organism stops, prevents or reduces the frequency, rate or extent of a process being mediated by a virus with which it is infected.
    GO:0032780    negative regulation of ATPase activity    Any process that stops or reduces the rate of ATP hydrolysis by an ATPase.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0031665    negative regulation of lipopolysaccharide-mediated signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
    GO:2001205    negative regulation of osteoclast development    Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development.
    GO:1900229    negative regulation of single-species biofilm formation in or on host organism    Any process that stops, prevents or reduces the frequency, rate or extent of single-species biofilm formation in or on host organism.
    GO:2000308    negative regulation of tumor necrosis factor (ligand) superfamily member 11 production    Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor (ligand) superfamily member 11 production.
    GO:0045071    negative regulation of viral genome replication    Any process that stops, prevents, or reduces the frequency, rate or extent of viral genome replication.
    GO:0048525    negative regulation of viral process    Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process in which a virus is a participant.
    GO:0001503    ossification    The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0051092    positive regulation of NF-kappaB transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of the transcription factor NF-kappaB.
    GO:1900159    positive regulation of bone mineralization involved in bone maturation    Any process that activates or increases the frequency, rate or extent of bone mineralization involved in bone maturation.
    GO:1902732    positive regulation of chondrocyte proliferation    Any process that increases the frequency, rate or extent of the multiplication or reproduction of chondrocytes by cell division, resulting in the expansion of their population. A chondrocyte is a polymorphic cell that forms cartilage.
    GO:0045669    positive regulation of osteoblast differentiation    Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
    GO:0033690    positive regulation of osteoblast proliferation    Any process that activates or increases the rate or extent of osteoblast proliferation.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0034145    positive regulation of toll-like receptor 4 signaling pathway    Any process that activates or increases the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001817    regulation of cytokine production    Any process that modulates the frequency, rate, or extent of production of a cytokine.
    GO:0032680    regulation of tumor necrosis factor production    Any process that modulates the frequency, rate, or extent of tumor necrosis factor production.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0030141    secretory granule    A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules.
    GO:0042581    specific granule    Granule with a membranous, tubular internal structure, found primarily in mature neutrophil cells. Most are released into the extracellular fluid. Specific granules contain lactoferrin, lysozyme, vitamin B12 binding protein and elastase.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TRFL_BOVIN | P246271blf 1lfc 1nkx 1sdx 1y58 2alu 2ays 2b65 2doj 2dp8 2dqv 2ds9 2dsf 2dvc 2dwa 2dwh 2dwi 2dwj 2dxr 2dxy 2dyx 2e0s 2e1s 2fa7 2g93 2h4i 2hca 2md1 2md2 2md3 2nuv 2nwj 2o1l 2o51 2ocu 2p1s 2px1 2q8j 2qje 2r71 2r9j 2zmb 3cfl 3ci8 3crb 3e9x 3iaz 3ib0 3ib1 3ib2 3k0v 3kj7 3mjn 3o97 3rgy 3sdf 3taj 3tod 3ttr 3tus 3u72 3u8q 3ugw 3uk4 3usd 3v5a 3vdf 4dig 4dxu 4fim 4fjp 4for 4g2z 4g77 4g8h 4grk 4n6p 4ned 4oqo 5cry 5hbc

(-) Related Entries Specified in the PDB File

2md1 2md2 2md3