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(-) Description

Title :  POLYGALACTURONASE FROM ASPERGILLUS ACULEATUS
 
Authors :  S. W. Cho, S. Lee, W. Shin
Date :  22 Mar 01  (Deposition) - 19 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Polygalacturonase, Glycosylhydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Cho, S. Lee, W. Shin
The X-Ray Structure Of Aspergillus Aculeatus Polygalacturonase And A Modeled Structure Of The Polygalacturonase-Octagalacturonate Complex.
J. Mol. Biol. V. 311 863 2001
PubMed-ID: 11518536  |  Reference-DOI: 10.1006/JMBI.2001.4919

(-) Compounds

Molecule 1 - POLYGALACTURONASE
    Chains: A
    EC Number: 3.2.1.15
    Organism Scientific: ASPERGILLUS ACULEATUS
    Organism Taxid: 5053

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1MAN11Ligand/IonALPHA-D-MANNOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:1 , THR A:3 , THR A:5BINDING SITE FOR RESIDUE MAN A 405
02AC2SOFTWARESER A:7 , THR A:317 , ASP A:318 , HOH A:585BINDING SITE FOR RESIDUE MAN A 407
03AC3SOFTWARESER A:9 , SER A:213 , ASN A:215 , THR A:216 , THR A:243 , GLY A:244 , SER A:245 , ASN A:290 , HIS A:292 , HOH A:617 , HOH A:632BINDING SITE FOR RESIDUE MAN A 409
04AC4SOFTWAREASN A:10 , SER A:13 , LYS A:17 , THR A:284 , MAN A:414 , MAN A:416 , HOH A:542 , HOH A:685BINDING SITE FOR RESIDUE MAN A 413
05AC5SOFTWAREALA A:1 , ASN A:10 , SER A:14 , MAN A:413 , MAN A:418 , HOH A:520 , HOH A:684 , HOH A:692BINDING SITE FOR RESIDUE MAN A 414
06AC6SOFTWARESER A:13 , SER A:16 , ASP A:39 , MAN A:413 , HOH A:595BINDING SITE FOR RESIDUE MAN A 416
07AC7SOFTWARETHR A:2 , PHE A:6 , SER A:14 , LYS A:17 , SER A:18 , MAN A:414 , MAN A:423BINDING SITE FOR RESIDUE MAN A 418
08AC8SOFTWAREALA A:1 , THR A:20 , CYS A:22 , SER A:23 , ASN A:44 , MAN A:418 , HOH A:527BINDING SITE FOR RESIDUE MAN A 423
09AC9SOFTWARETHR A:3 , THR A:24 , HIS A:48BINDING SITE FOR RESIDUE MAN A 424
10BC1SOFTWARESER A:34 , TYR A:59 , LYS A:60 , THR A:167 , GLU A:189 , ASN A:190 , HOH A:601 , HOH A:619BINDING SITE FOR RESIDUE MAN A 434
11BC2SOFTWAREASN A:190 , ASN A:219 , NAG A:352 , HOH A:521 , HOH A:579 , HOH A:619BINDING SITE FOR RESIDUE NAG A 351
12BC3SOFTWARETYR A:168 , NAG A:351 , MAN A:353BINDING SITE FOR RESIDUE NAG A 352
13BC4SOFTWARENAG A:352BINDING SITE FOR RESIDUE MAN A 353

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:22
2A:182 -A:198
3A:306 -A:311
4A:330 -A:339

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:64 -Pro A:65
2Gly A:207 -Ser A:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IA5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1POLYGALACTURONASEPS00502 Polygalacturonase active site.PGLR1_ASPAC234-247  1A:195-208

(-) Exons   (0, 0)

(no "Exon" information available for 1IA5)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:339
 aligned with PGLR1_ASPAC | O74213 from UniProtKB/Swiss-Prot  Length:378

    Alignment length:339
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369         
          PGLR1_ASPAC    40 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 378
               SCOP domains d1ia5a_ A: Polygalacturonase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1ia5A00 A:1-339 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhh.eeeee..ee.....eee.......eeeee.eeee.........eeeeee..eeee....eee.hhhhh...............eeeeeeeeeeee..eee......eeee..eeeeee..eee.hhhh.........eeee..eeeeee..eee.....eee..eeeeeee..eee....eeeeee......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeeeeeeeee..eeeeeeeee............eeeeeeeeeeeee....eeeeee.....eeeeeeeeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------POLYGALACTURON----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ia5 A   1 ATTCTFSGSNGASSASKSKTSCSTIVLSNVAVPSGTTLDLTKLNDGTHVIFSGETTFGYKEWSGPLISVSGSDLTITGASGHSINGDGSRWWDGEGGNGGKTKPKFFAAHSLTNSVISGLKIVNSPVQVFSVAGSDYLTLKDITIDNSDGDDNGGHNTDAFDIGTSTYVTISGATVYNQDDCVAVNSGENIYFSGGYCSGGHGLSIGSVGGRSDNTVKNVTFVDSTIINSDNGVRIKTNIDTTGSVSDVTYKDITLTSIAKYGIVVQQNYGDTSSTPTTGVPITDFVLDNVHGSVVSSGTNILISCGSGSCSDWTWTDVSVSGGKTSSKCTNVPSGASC 339
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IA5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PGLR1_ASPAC | O74213)
molecular function
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004650    polygalacturonase activity    Catalysis of the random hydrolysis of (1->4)-alpha-D-galactosiduronic linkages in pectate and other galacturonans.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGLR1_ASPAC | O74213: 1ib4

(-) Related Entries Specified in the PDB File

1bhe 1BHE CONTAINS THE SAME PROTEIN FROM ERWINIA CAROTOVORA SSP.CAROTOVORA
1czf 1CZF CONTAINS ENDO-POLYGALACTURONASE II FROM ASPERGILLUS NIGER
1ib4 1IB4 CONTAINS THE SAME PROTEIN AT PH4.5
1rmg 1RMG CONTAINS RHAMNOGALACTURONASE A