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(-) Description

Title :  HIGHER-DENSITY CRYSTAL STRUCTURE OF POTATO ENDO-1,3-BETA-GLUCANASE
 
Authors :  A. Wojtkowiak, K. Witek, J. Hennig, M. Jaskolski
Date :  21 Nov 11  (Deposition) - 30 May 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glucoside Hydrolase, Gh17 Family, Pathogenesis-Related Class-2 Protein (Pr-2), Tim Barrel, Hydrolase, Carbohydrate/Sugar Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Wojtkowiak, K. Witek, J. Hennig, M. Jaskolski
Two High-Resolution Structures Of Potato Endo-1, 3-Beta-Glucanase Reveal Subdomain Flexibility With Implications For Substrate Binding
Acta Crystallogr. , Sect. D V. 68 713 2012
PubMed-ID: 22683794  |  Reference-DOI: 10.1107/S090744491200995X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCAN ENDO-1,3-BETA-D-GLUCOSIDASE
    Chains: A, B
    EC Number: 3.2.1.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-30A(+)
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: MATURE ENDO-1,3-BETA-GLUCANASE, UNP RESIDUES 24-338
    Gene: GLUB20-2
    Organism Common: POTATOES
    Organism Scientific: SOLANUM TUBEROSUM
    Organism Taxid: 4113
    Strain: DESIREE
    Synonym: 1,3-BETA-D-GLUCAN GLUCANOHYDROLASE, ENDO-1,3-BETA-GLUCANASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:35 , GLY B:249 , GLN B:251 , HOH B:630BINDING SITE FOR RESIDUE NA B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3UR7)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:105 -Pro A:106
2Tyr A:167 -Pro A:168
3Phe A:305 -Ala A:306
4Phe B:105 -Pro B:106
5Tyr B:167 -Pro B:168
6Phe B:305 -Ala B:306

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3UR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3UR7)

(-) Exons   (0, 0)

(no "Exon" information available for 3UR7)

(-) Sequences/Alignments

Asymmetric 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:316
 aligned with Q70C53_SOLTU | Q70C53 from UniProtKB/TrEMBL  Length:338

    Alignment length:316
                                                                                                                                                                                                                                                                                                                                                    338 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    | 
         Q70C53_SOLTU    24 QPIGVCYGKIANNLPSDQDVIKLYNANNIKKMRIYYPHTNVFNALKGSNIEIILDVPNQDLEALANPSNANGWVQDNIRNHFPDVKFKYIAVGNEVDPGRESGKYARFVGPAMENIYNALSSAGLQNQIKVSTSTYSGLLTNTYPPRDSIFREEYKSFINPIIGFLARHNLPLLANIYPYFGHIDNTNAVPLSYALFNQQRRNDTGYQNLFDALVDSMYFATEKLGGQNIEIIVSESGWPSEGHPAATLKNARTYYTNLINHVKRGAGTPKKPGKTIETYLFAMFDENEKKGEASEKHFGLFNPDQRPKYQLNFN-   -
               SCOP domains d3ur7a_ A: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........hhhhhhhhhhhh...eeee...hhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee...ee...hhhhhee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhh.......eeeeee..........hhhhhhhhhhhhhhhhhh.............eee...........hhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ur7 A  24 QPIGVCYGKIANNLPSDQDVIKLYNANNIKKMRIYYPHTNVFNALKGSNIEIILDVPNQDLEALANPSNANGWVQDNIRNHFPDVKFKYIAVGNEVDPGRESGKYARFVGPAMENIYNALSSAGLQNQIKVSTSTYSGLLTNTYPPRDSIFREEYKSFINPIIGFLARHNLPLLANIYPYFGHIDNTNAVPLSYALFNQQRRNDTGYQNLFDALVDSMYFATEKLGGQNIEIIVSESGWPSEGHPAATLKNARTYYTNLINHVKRGAGTPKKPGKTIETYLFAMFDENEKKGEASEKHFGLFNPDQRPKYQLNFNH 344
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    ||
                                                                                                                                                                                                                                                                                                                                                    338|
                                                                                                                                                                                                                                                                                                                                                     344


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with Q70C53_SOLTU | Q70C53 from UniProtKB/TrEMBL  Length:338

    Alignment length:316
                                                                                                                                                                                                                                                                                                                                                    338 
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    | 
         Q70C53_SOLTU    24 QPIGVCYGKIANNLPSDQDVIKLYNANNIKKMRIYYPHTNVFNALKGSNIEIILDVPNQDLEALANPSNANGWVQDNIRNHFPDVKFKYIAVGNEVDPGRESGKYARFVGPAMENIYNALSSAGLQNQIKVSTSTYSGLLTNTYPPRDSIFREEYKSFINPIIGFLARHNLPLLANIYPYFGHIDNTNAVPLSYALFNQQRRNDTGYQNLFDALVDSMYFATEKLGGQNIEIIVSESGWPSEGHPAATLKNARTYYTNLINHVKRGAGTPKKPGKTIETYLFAMFDENEKKGEASEKHFGLFNPDQRPKYQLNFN-   -
               SCOP domains d3ur7b_ B: automated matches                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.........hhhhhhhhhhhh...eeee...hhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee...ee...hhhhhee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhh....hhhhhh............hhhhhhhhhhhhhhhhh......eeeeee..........hhhhhhhhhhhhhhhhhhh............eee...........hhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ur7 B  24 QPIGVCYGKIANNLPSDQDVIKLYNANNIKKMRIYYPHTNVFNALKGSNIEIILDVPNQDLEALANPSNANGWVQDNIRNHFPDVKFKYIAVGNEVDPGRESGKYARFVGPAMENIYNALSSAGLQNQIKVSTSTYSGLLTNTYPPRDSIFREEYKSFINPIIGFLARHNLPLLANIYPYFGHIDNTNAVPLSYALFNQQRRNDTGYQNLFDALVDSMYFATEKLGGQNIEIIVSESGWPSEGHPAATLKNARTYYTNLINHVKRGAGTPKKPGKTIETYLFAMFDENEKKGEASEKHFGLFNPDQRPKYQLNFNH 344
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    ||
                                                                                                                                                                                                                                                                                                                                                    338|
                                                                                                                                                                                                                                                                                                                                                     344
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3UR7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3UR7)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q70C53_SOLTU | Q70C53)
molecular function
    GO:0042973    glucan endo-1,3-beta-D-glucosidase activity    Catalysis of the hydrolysis of (1->3)-beta-D-glucosidic linkages in (1->3)-beta-D-glucans.
    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:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
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: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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q70C53_SOLTU | Q70C53: 3ur8 4gzi 4gzj

(-) Related Entries Specified in the PDB File

1ghs THE THREE-DIMENSIONAL STRUCTURES OF TWO PLANT BETA-GLUCAN ENDOHYDROLASES WITH DISTINCT SUBSTRATE SPECIFICITIES
2cyg CRYSTAL STRUCTURE AT 1.45- RESOLUTION OF THE MAJOR ALLERGEN ENDO-BETA-1,3-GLUCANASE OF BANANA AS A MOLECULAR BASIS FOR THE LATEX-FRUIT SYNDROME
3em5 CRYSTAL STRUCTURE OF A NATIVE ENDO BETA-1,3-GLUCANASE (HEV B 2), A MAJOR ALLERGEN FROM HEVEA BRASILIENSIS
3f55 CRYSTAL STRUCTURE OF THE NATIVE ENDO BETA-1,3-GLUCANASE (HEV B 2), A MAJOR ALLERGEN FROM HEVEA BRASILIENSIS (SPACE GROUP P41)
3ur8 LOWER-DENSITY CRYSTAL STRUCTURE OF POTATO ENDO-1,3-BETA- GLUCANASE