2fh8

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure Analysis of Klebsiella pneumoniae pullulanase complexed with isomaltose

Structural highlights

2fh8 is a 1 chain structure with sequence from Klebsiella pneumoniae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

W9BQ28_KLEPN

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 crystal structures of Klebsiella pneumoniae pullulanase and its complex with glucose (G1), maltose (G2), isomaltose (isoG2), maltotriose (G3), or maltotetraose (G4), have been refined at around 1.7-1.9A resolution by using a synchrotron radiation source at SPring-8. The refined models contained 920-1052 amino acid residues, 942-1212 water molecules, four or five calcium ions, and the bound sugar moieties. The enzyme is composed of five domains (N1, N2, N3, A, and C). The N1 domain was clearly visible only in the structure of the complex with G3 or G4. The N1 and N2 domains are characteristic of pullulanase, while the N3, A, and C domains have weak similarity with those of Pseudomonas isoamylase. The N1 domain was found to be a new type of carbohydrate-binding domain with one calcium site (CBM41). One G1 bound at subsite -2, while two G2 bound at -1 approximately -2 and +2 approximately +1, two G3, -1 approximately -3 and +2 approximately 0', and two G4, -1 approximately -4 and +2 approximately -1'. The two bound G3 and G4 molecules in the active cleft are almost parallel and interact with each other. The subsites -1 approximately -4 and +1 approximately +2, including catalytic residues Glu706 and Asp677, are conserved between pullulanase and alpha-amylase, indicating that pullulanase strongly recognizes branched point and branched sugar residues, while subsites 0' and -1', which recognize the non-reducing end of main-chain alpha-1,4 glucan, are specific to pullulanase and isoamylase. The comparison suggested that the conformational difference around the active cleft, together with the domain organization, determines the different substrate specificities between pullulanase and isoamylase.

Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site.,Mikami B, Iwamoto H, Malle D, Yoon HJ, Demirkan-Sarikaya E, Mezaki Y, Katsuya Y J Mol Biol. 2006 Jun 9;359(3):690-707. Epub 2006 Apr 18. PMID:16650854^[1]

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

References

↑ Mikami B, Iwamoto H, Malle D, Yoon HJ, Demirkan-Sarikaya E, Mezaki Y, Katsuya Y. Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site. J Mol Biol. 2006 Jun 9;359(3):690-707. Epub 2006 Apr 18. PMID:16650854 doi:10.1016/j.jmb.2006.03.058

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/2fh8"

@@ Line 1: / Line 1: @@
 ==Crystal Structure Analysis of Klebsiella pneumoniae pullulanase complexed with isomaltose==
-<StructureSection load='2fh8' size='340' side='right' caption='[[2fh8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2fh8' size='340' side='right'caption='[[2fh8]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fh8]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Klebsiella_aerogenes Klebsiella aerogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FH8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FH8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fh8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FH8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FH8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2fgz|2fgz]], [[2fh6|2fh6]], [[2fhb|2fhb]], [[2fhc|2fhc]], [[2fhf|2fhf]]</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pullulanase Pullulanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.41 3.2.1.41] </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=2fh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fh8 OCA], [https://pdbe.org/2fh8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fh8 RCSB], [https://www.ebi.ac.uk/pdbsum/2fh8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fh8 ProSAT]</span></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=2fh8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fh8 OCA], [http://pdbe.org/2fh8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fh8 RCSB], [http://www.ebi.ac.uk/pdbsum/2fh8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fh8 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/W9BQ28_KLEPN W9BQ28_KLEPN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fh/2fh8_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fh/2fh8_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>
   </jmolCheckbox>
@@ Line 28: / Line 29: @@
 </div>
 <div class="pdbe-citations 2fh8" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Amylase 3D structures|Amylase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Klebsiella aerogenes]]
+[[Category: Klebsiella pneumoniae]]
-[[Category: Pullulanase]]
+[[Category: Large Structures]]
-[[Category: Demirkan-Sarikaya, E]]
+[[Category: Demirkan-Sarikaya E]]
-[[Category: Iwamoto, H]]
+[[Category: Iwamoto H]]
-[[Category: Katsuya, Y]]
+[[Category: Katsuya Y]]
-[[Category: Malle, D]]
+[[Category: Malle D]]
-[[Category: Mikami, B]]
+[[Category: Mikami B]]
-[[Category: Yoon, H J]]
+[[Category: Yoon H-J]]
-[[Category: Alpha-amylase-family]]
-[[Category: Beta-alpha-barrel]]
-[[Category: Complex with isomaltose]]
-[[Category: Hydrolase]]
-[[Category: Multiple domain]]

2fh8

From Proteopedia

Current revision

Crystal Structure Analysis of Klebsiella pneumoniae pullulanase complexed with isomaltose

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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