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KEGG pathways | MAP code | Pathways |
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MAP00040 | Pentose and glucuronate interconversions | MAP00500 | Starch and sucrose metabolism |
UniProtKB:Accession Number | P26509 | O74213 | P26213 | P26214 | P79074 | Q07181 |
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Entry name | PGLR2_PECCC | PGLR1_ASPAC | PGLR1_ASPNG | PGLR2_ASPNG | P79074_9AGAR | PGLR_GIBFU |
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Activity | Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans. | Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans. | Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans. | Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans. |
| Random hydrolysis of (1->4)-alpha-D- galactosiduronic linkages in pectate and other galacturonans. |
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Subunit | Monomer. |
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Subcellular location | Secreted. |
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References for Catalytic Mechanism | References | Sections | No. of steps in catalysis |
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[1] | Scheme 1, p.171-172 |
| [3] | p.538-539 |
| [4] | p.24664 |
| [5] | Fig.3, p.30477-30479 |
| [6] | p.695-696 |
| [10] | p.870-874 |
| [11] | p.13429-13430 |
| [13] | Fig.7, p.6656-6658 |
| [15] | p.60-61 |
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references | [1] |
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PubMed ID | 1416030 |
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Journal | Anal Biochem |
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Year | 1992 |
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Volume | 203 |
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Pages | 335-9 |
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Authors | Bach E, Schollmeyer E |
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Title | An ultraviolet-spectrophotometric method with 2-cyanoacetamide for the determination of the enzymatic degradation of reducing polysaccharides. |
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[2] |
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PubMed ID | 8814223 |
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Journal | Biochim Biophys Acta |
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Year | 1996 |
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Volume | 1296 |
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Pages | 167-73 |
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Authors | Rao MN, Kembhavi AA, Pant A |
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Title | Implication of tryptophan and histidine in the active site of endo-polygalacturonase from Aspergillus ustus: elucidation of the reaction mechanism. |
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[3] |
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PubMed ID | 9115442 |
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Journal | Structure |
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Year | 1997 |
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Volume | 5 |
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Pages | 533-44 |
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Authors | Petersen TN, Kauppinen S, Larsen S |
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Title | The crystal structure of rhamnogalacturonase A from Aspergillus aculeatus: a right-handed parallel beta helix. |
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[4] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS). |
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Medline ID | 98406113 |
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PubMed ID | 9733763 |
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Journal | J Biol Chem |
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Year | 1998 |
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Volume | 273 |
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Pages | 24660-4 |
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Authors | Pickersgill R, Smith D, Worboys K, Jenkins J |
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Title | Crystal structure of polygalacturonase from Erwinia carotovora ssp. carotovora. |
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Related PDB | 1bhe |
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Related UniProtKB | P26509 |
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[5] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS), AND MUTAGENESIS OF ASP-180; ASP-201; ASP-202; HIS-223; ARG-256 AND LYS-258. |
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PubMed ID | 10521427 |
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Journal | J Biol Chem |
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Year | 1999 |
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Volume | 274 |
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Pages | 30474-80 |
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Authors | van Santen Y, Benen JA, Schroter KH, Kalk KH, Armand S, Visser J, Dijkstra BW |
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Title | 1.68-A crystal structure of endopolygalacturonase II from Aspergillus niger and identification of active site residues by site-directed mutagenesis. |
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Related PDB | 1czf |
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Related UniProtKB | P26214 |
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[6] |
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PubMed ID | 10617668 |
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Journal | J Biol Chem |
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Year | 2000 |
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Volume | 275 |
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Pages | 691-6 |
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Authors | Armand S, Wagemaker MJ, Sanchez-Torres P, Kester HC, van Santen Y, Dijkstra BW, Visser J, Benen JA |
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Title | The active site topology of Aspergillus niger endopolygalacturonase II as studied by site-directed mutagenesis. |
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[7] |
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PubMed ID | 10893426 |
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Journal | J Biol Chem |
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Year | 2000 |
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Volume | 275 |
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Pages | 29348-53 |
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Authors | Pages S, Heijne WH, Kester HC, Visser J, Benen JA |
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Title | Subsite mapping of Aspergillus niger endopolygalacturonase II by site-directed mutagenesis. |
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[8] |
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PubMed ID | 11168425 |
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Journal | Eur J Biochem |
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Year | 2001 |
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Volume | 268 |
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Pages | 832-40 |
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Authors | Niture SK, Pant A, Kumar AR |
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Title | Active site characterization of the single endo-polygalacturonase produced by Fusarium moniliforme NCIM 1276. |
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[9] |
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PubMed ID | 11445590 |
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Journal | J Biol Chem |
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Year | 2001 |
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Volume | 276 |
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Pages | 33652-6 |
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Authors | Pages S, Kester HC, Visser J, Benen JA |
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Title | Changing a single amino acid residue switches processive and non-processive behavior of Aspergillus niger endopolygalacturonase I and II. |
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[10] |
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Comments | X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 40-378, AND GLYCOSYLATION AT THR-44; SER-46; SER-48; SER-52; SER-53; SER-55; SER-57; SER-62; THR-63; SER-73 AND ASN-249. |
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PubMed ID | 11518536 |
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Journal | J Mol Biol |
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Year | 2001 |
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Volume | 311 |
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Pages | 863-78 |
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Authors | Cho SW, Lee S, Shin W |
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Title | The X-ray structure of Aspergillus aculeatus polygalacturonase and a modeled structure of the polygalacturonase-octagalacturonate complex. |
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Related PDB | 1ia5,1ib4 |
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Related UniProtKB | O74213 |
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[11] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF 25-373, AND MUTAGENESIS OF HIS-188; ASP-191; 212-ASP-ASP-213; ARG-267 AND LYS-269. |
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PubMed ID | 11687632 |
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Journal | Proc Natl Acad Sci U S A |
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Year | 2001 |
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Volume | 98 |
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Pages | 13425-30 |
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Authors | Federici L, Caprari C, Mattei B, Savino C, Di Matteo A, De Lorenzo G, Cervone F, Tsernoglou D |
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Title | Structural requirements of endopolygalacturonase for the interaction with PGIP (polygalacturonase-inhibiting protein). |
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Related PDB | 1hg8 |
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Related UniProtKB | Q07181 |
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[12] |
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PubMed ID | 11707607 |
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Journal | Protein Eng |
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Year | 2001 |
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Volume | 14 |
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Pages | 615-31 |
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Authors | Markovic O, Janecek S |
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Title | Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution. |
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[13] |
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Comments | X-RAY CRYSTALLOGRAPHY (0.96 ANGSTROMS) OF 25-359. |
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PubMed ID | 12022868 |
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Journal | Biochemistry |
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Year | 2002 |
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Volume | 41 |
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Pages | 6651-9 |
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Authors | Shimizu T, Nakatsu T, Miyairi K, Okuno T, Kato H |
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Title | Active-site architecture of endopolygalacturonase I from Stereum purpureum revealed by crystal structures in native and ligand-bound forms at atomic resolution. |
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Related PDB | 1k5c,1kcc,1kcd |
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Related UniProtKB | P79074 |
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[14] |
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Comments | X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 33-368, AND GLYCOSYLATION AT SER-44; SER-46 AND ASN-246. |
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PubMed ID | 14623112 |
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Journal | FEBS Lett |
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Year | 2003 |
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Volume | 554 |
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Pages | 462-6 |
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Authors | van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW |
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Title | Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. |
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Related PDB | 1nhc |
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Related UniProtKB | P26213 |
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[15] |
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PubMed ID | 15848136 |
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Journal | Biochim Biophys Acta |
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Year | 2005 |
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Volume | 1749 |
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Pages | 53-64 |
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Authors | Andre-Leroux G, Tessier D, Bonnin E |
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Title | Action pattern of Fusarium moniliforme endopolygalacturonase towards pectin fragments: Comprehension and prediction. |
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comments | This enzyme belongs to the glycosidase family-28, with an inverting mechanism. According to the literature [13], the distances between the three catalytic residues with a carboxy group in the sidechain (Asp153, Asp173, Asp174) are all approximately 5 A, although the distances between the catalytic carboxy groups should be approximately 10 A in the ordinary inverting glycosidases. The difference of the catalytic site of this glycosidase enzyme from those of the other enzymes might suggest some differenes in its catalytic mechanism from those by other enzymes. According to the literature [13], the reaction proceeds by SN2-like reaction, for this enzyme, unlike the other glycosidase enzymes. According to the literature [13], the reaction of this enzyme proceeds as follows: (0) Lys228 and Arg226 (of 1k5c) modulate and decrease the pKa of Asp174, one of general bases, whilst Asp156 modulate the pKa of Asp153, another base. (1) Asp174 and Asp153 act as general bases, which deprotonate and activate the hydrolytic water. (Asp174 is more likely to be a general base than Asp153.) (2) The activated water makes a nucleophilic attack on anomeric carbon of the scissile bond. The reaction proceeds by an SN2-like mechanism. (3) Asp173 acts as a general acid to protonate the leaving group, the glycosidic oxygen, completing the hydrolysis.
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created | updated |
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2007-01-05 | 2009-02-26 |
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