1rh9: Difference between revisions

Revision as of 07:24, 25 October 2023

Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato)

Structural highlights

1rh9 is a 1 chain structure with sequence from Solanum lycopersicum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.5Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MAN4_SOLLC Possesses endo-beta-mannanase and mannan transglycosylase activities. May be involved in cell wall degradation during fruit ripening.^[1] ^[2]

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

The three-dimensional crystal structure of tomato (Lycopersicon esculentum) beta-mannanase 4a (LeMAN4a) has been determined to 1.5 A resolution. The enzyme adopts the (beta/alpha)(8) fold common to the members of glycohydrolase family GH5. The structure is comparable with those of the homologous Trichoderma reesei and Thermomonospora fusca beta-mannanases: There is a conserved three-stranded beta-sheet located near the N terminus that stacks against the central beta-barrel at the end opposite the active site. Three noncanonical beta-helices surround the active site. Similar helices are found in T. reesei but not T. fusca beta-mannanase. By analogy with other beta-mannanases, the catalytic acid/base residue is E204 and the nucleophile residue is E318. The active site cleft of L. esculentum beta-mannanase most closely resembles that of the T. reesei isozyme. A model of substrate binding in LeMAN4a is proposed in which the mannosyl residue occupying the -1 subsite of the enzyme adopts the (1)S(5) skew-boat conformation.

Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit.,Bourgault R, Oakley AJ, Bewley JD, Wilce MC Protein Sci. 2005 May;14(5):1233-41. PMID:15840830^[3]

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

References

↑ Bourgault R, Bewley JD. Variation in its C-terminal amino acids determines whether endo-beta-mannanase is active or inactive in ripening tomato fruits of different cultivars. Plant Physiol. 2002 Nov;130(3):1254-62. PMID:12427992 doi:https://dx.doi.org/10.1104/pp.011890
↑ Schroder R, Wegrzyn TF, Sharma NN, Atkinson RG. LeMAN4 endo-beta-mannanase from ripe tomato fruit can act as a mannan transglycosylase or hydrolase. Planta. 2006 Oct;224(5):1091-102. Epub 2006 Apr 29. PMID:16649044 doi:https://dx.doi.org/10.1007/s00425-006-0286-0
↑ Bourgault R, Oakley AJ, Bewley JD, Wilce MC. Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit. Protein Sci. 2005 May;14(5):1233-41. PMID:15840830 doi:14/5/1233

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Bourgault R, Bewley JD. Variation in its C-terminal amino acids determines whether endo-beta-mannanase is active or inactive in ripening tomato fruits of different cultivars. Plant Physiol. 2002 Nov;130(3):1254-62. PMID:12427992 doi:https://dx.doi.org/10.1104/pp.011890

[2] Schroder R, Wegrzyn TF, Sharma NN, Atkinson RG. LeMAN4 endo-beta-mannanase from ripe tomato fruit can act as a mannan transglycosylase or hydrolase. Planta. 2006 Oct;224(5):1091-102. Epub 2006 Apr 29. PMID:16649044 doi:https://dx.doi.org/10.1007/s00425-006-0286-0

[3] Bourgault R, Oakley AJ, Bewley JD, Wilce MC. Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit. Protein Sci. 2005 May;14(5):1233-41. PMID:15840830 doi:14/5/1233

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='1rh9' size='340' side='right'caption='[[1rh9]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rh9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RH9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RH9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rh9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RH9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RH9 FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1bqc|1bqc]], [[1qnp|1qnp]]</div></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]] 1.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LeMAN4a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=1rh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rh9 OCA], [https://pdbe.org/1rh9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rh9 RCSB], [https://www.ebi.ac.uk/pdbsum/1rh9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rh9 ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannan_endo-1,4-beta-mannosidase Mannan endo-1,4-beta-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.78 3.2.1.78] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1rh9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rh9 OCA], [http://pdbe.org/1rh9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rh9 RCSB], [http://www.ebi.ac.uk/pdbsum/1rh9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rh9 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MAN4_SOLLC MAN4_SOLLC]] Possesses endo-beta-mannanase and mannan transglycosylase activities. May be involved in cell wall degradation during fruit ripening.<ref>PMID:12427992</ref> <ref>PMID:16649044</ref>
+[https://www.uniprot.org/uniprot/MAN4_SOLLC MAN4_SOLLC] Possesses endo-beta-mannanase and mannan transglycosylase activities. May be involved in cell wall degradation during fruit ripening.<ref>PMID:12427992</ref> <ref>PMID:16649044</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 38: / Line 36: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lycopersicon esculentum]]
+[[Category: Solanum lycopersicum]]
-[[Category: Mannan endo-1,4-beta-mannosidase]]
+[[Category: Bewley JD]]
-[[Category: Bewley, J D]]
+[[Category: Bourgault R]]
-[[Category: Bourgault, R]]
+[[Category: Oakley AJ]]
-[[Category: Oakley, A J]]
+[[Category: Wilce MCJ]]
-[[Category: Wilce, M C.J]]
-[[Category: Endo-beta-mannase]]
-[[Category: Glycoside hydrolase family 5]]
-[[Category: Hydrolase]]
-[[Category: Mannan]]
-[[Category: Retaining]]

1rh9: Difference between revisions

Revision as of 07:24, 25 October 2023

Family GH5 endo-beta-mannanase from Lycopersicon esculentum (tomato)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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