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(-) Description

Title :  ENDOPOLYGALACTURONASE I FROM STEREUM PURPUREUM COMPLEXED WITH A GALACTURONATE AT 1.00 A RESOLUTION.
 
Authors :  T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno, H. Kato
Date :  08 Nov 01  (Deposition) - 05 Jun 02  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Helical Structure, Glycoside Hydrolase, Silver-Leaf Inducing Substance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Shimizu, T. Nakatsu, K. Miyairi, T. Okuno, H. Kato
Active-Site Architecture Of Endopolygalacturonase I From Stereum Purpureum Revealed By Crystal Structures In Native And Ligand-Bound Forms At Atomic Resolution.
Biochemistry V. 41 6651 2002
PubMed-ID: 12022868  |  Reference-DOI: 10.1021/BI025541A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPOLYGALACTURONASE
    Chains: A
    EC Number: 3.2.1.15
    Fragment: RESIDUES 1-335
    Organism Scientific: CHONDROSTEREUM PURPUREUM
    Organism Taxid: 58369
    Strain: ASP-4B

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GTR1Ligand/IonBETA-D-GALACTOPYRANURONIC ACID
3NA1Ligand/IonSODIUM ION
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:91 , HIS A:150 , ASN A:151 , ASP A:173 , HIS A:195 , ARG A:226 , LYS A:228 , TYR A:262 , HOH A:2024 , HOH A:2190 , HOH A:2210 , HOH A:2293 , HOH A:2391BINDING SITE FOR RESIDUE GTR A 1001
2AC2SOFTWAREASP A:13 , LYS A:88 , ASN A:92 , HOH A:2500 , HOH A:2518 , HOH A:2586BINDING SITE FOR RESIDUE NAG A 2001
3AC3SOFTWAREASN A:160 , ASN A:161 , ASN A:182 , HOH A:2185BINDING SITE FOR RESIDUE NAG A 2002
4AC4SOFTWAREGLY A:30 , THR A:54 , THR A:55 , ASN A:308BINDING SITE FOR RESIDUE CL A 2003
5AC5SOFTWAREASP A:156 , SER A:158 , ASN A:179BINDING SITE FOR RESIDUE NA A 2004

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:17
2A:175 -A:191
3A:300 -A:303

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:58 -Pro A:59
2His A:98 -Pro A:99
3Gly A:125 -Pro A:126
4Gly A:200 -Ser A:201
5Tyr A:262 -Pro A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KCC)

(-) Exons   (0, 0)

(no "Exon" information available for 1KCC)

(-) 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:333
 aligned with P79074_9AGAR | P79074 from UniProtKB/TrEMBL  Length:403

    Alignment length:333
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356   
         P79074_9AGAR    27 CTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLKIKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIAKYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGNCSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL 359
               SCOP domains d1kcca_ A: Polygalacturonase                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1kccA00 A:3-335 Single-stranded right-handed beta-helix, Pectin lyase-like                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhh....eeee..eee.....eee......eeee...eee.........eeeeeeeeeee....eee.hhhhh................eeeeeeeeee..eee......eeeeeeeeeeeee..eee.hhhhhhhh......eeee...eeee..eee.....eeeeeeeeeeee..eee....eeeeee....eeeeeeee..eeeeeeeeeeeeee......eeeeeeee..eeeeeeeeeeeeeeee............eeeeee....eeeee....eeeeee...ee.eee...eeee......ee....eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kcc A   3 CTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLKIKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIAKYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGNCSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL 335
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
   Legend:   → Mismatch (orange background)
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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 1KCC)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (P79074_9AGAR | P79074)
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/TrEMBL
        P79074_9AGAR | P79074: 1k5c 1kcd

(-) Related Entries Specified in the PDB File

1k5c 1K5C CONTAINS AN UNLIGANDED STRUCTURE OF THE SAME ENZYME.
1kcd 1KCD CONTAINS THE SAME ENZYME COMPLEXED WITH TWO GALACTURONATE.