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| [[Image:2d12.gif|left|200px]]<br /><applet load="2d12" size="350" color="white" frame="true" align="right" spinBox="true" | | #REDIRECT [[2zqn]] This PDB entry is obsolete and replaced by 2zqn |
| caption="2d12, resolution 1.90Å" />
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| '''Crystal structure of the earthworm R-type lectin C-half'''<br />
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| ==Overview==
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| Novel type lectins were found in the phylum Annelida, i.e. in the earthworm, tubifex, leech, and lugworm. The lectins (29-31 kDa) were extracted from the worms without the use of detergent and purified by affinity chromatography on asialofetuin-agarose. On the basis of the partial primary structures of the earthworm Lumbricus terrestris 29-kDa lectin (EW29), degenerate primers were synthesized for use in the reverse transcriptase-polymerase chain reaction. An amplified 155-base pair fragment was used to screen a cDNA library. Four types of full-length clones were obtained, all of which encoded 260 amino acids, but which were found to differ at 29 nucleotide positions. Since three of them resulted in non-silent substitutions, EW29 mRNA was considered to be a mixture of at least three distinct polynucleotides encoding the following proteins: Ala44-Gln197-Ile213 (clone 5), Gly44-Gln197-Val213 (clone 7), and Ala44-His197-Ile213 (clones 8 and 9; different at the nucleotide level, but encoding an identical polypeptide). Genomic polymerase chain reaction using DNA from a single worm revealed that the single worm already had four sets of cDNAs. The EW29 protein showed two features. First, the lectin was composed of two homologous domains (14,500 Da) showing 27% identity with each other. When each of the domains was separately expressed in Escherichia coli, the C-terminal domain was found to bind to asialofetuin-agarose as strongly as the whole protein, whereas the N-terminal domain did not bind and only retardation was observed. EW29 was found to exist as a monomer under non-denaturing conditions. It had significant hemagglutinating activity, which was inhibited by a wide range of galactose-containing saccharides. Second, EW29 contained multiple short conserved motifs, "Gly-X-X-X-Gln-X-Trp." Similar motifs have been found in many carbohydrate-recognizing proteins from an extensive variety of organisms, e.g. plant lectin ricin B-chain and Clostridium botulinum 33-kDa hemagglutinin. Therefore, these carbohydrate-recognition proteins appear to form a protein superfamily.
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| ==About this Structure==
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| 2D12 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Lumbricus_terrestris Lumbricus terrestris] with <scene name='pdbligand=PO4:'>PO4</scene> and <scene name='pdbligand=IMD:'>IMD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D12 OCA].
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| ==Reference==
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| Novel galactose-binding proteins in Annelida. Characterization of 29-kDa tandem repeat-type lectins from the earthworm Lumbricus terrestris., Hirabayashi J, Dutta SK, Kasai K, J Biol Chem. 1998 Jun 5;273(23):14450-60. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9603958 9603958]
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| [[Category: Lumbricus terrestris]]
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| [[Category: Single protein]]
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| [[Category: Fujimoto, Z.]]
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| [[Category: Hasegawa, T.]]
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| [[Category: Hirabayashi, J.]]
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| [[Category: Kasai, K.]]
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| [[Category: Kuno, A.]]
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| [[Category: Momma, M.]]
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| [[Category: Suzuki, R.]]
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| [[Category: IMD]]
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| [[Category: PO4]]
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| [[Category: beta-trefoil fold]]
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| [[Category: earthworm lumbricus terrestris]]
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| [[Category: hemagglutinin]]
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| [[Category: r-type lectin]]
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| [[Category: sugar complex]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:54:18 2008''
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This PDB entry is obsolete and replaced by 2zqn