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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC NUCLEOPHILE MUTANT OF VVEG16 IN COMPLEX WITH A XYLOGLUCAN TETRADECASACCHARIDE
 
Authors :  N. G. S. Mcgregor, C. C. Tung, F. Van Petegem, H. Brumer
Date :  25 Sep 15  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cell Wall, Dietary Fiber, Mixed-Linkage Glucan, Xyloglucan, Beta- Glucan, Glycoside Hydrolase, Endo-Glucanase, Grapes, Plants, Protein Structure, Gh16, Beta-Jelly Roll, Phylogeny, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. G. S. Mcgregor, C. C. Tung, V. Yin, F. Van Petegem, H. Brumer
Gh16 Plant Endoglucanases: Complete Structural And Functional Characterization Of A Representative Member Of The Mixed-Linkage Glucan Degrading Eg16 Family
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VVEG16, ENDO-GLUCANASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3) HI-CONTROL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ENDO-GLUCANASE
    Gene: VIT_15S0048G01850
    Mutation: YES
    Organism Common: GRAPE
    Organism Scientific: VITIS VINIFERA
    Organism Taxid: 29760

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric/Biological Unit (3, 21)
No.NameCountTypeFull Name
1BGC10Ligand/IonBETA-D-GLUCOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3XYS9Ligand/IonXYLOPYRANOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:21 , HIS A:41 , ARG A:42 , GLY A:43 , ARG A:46 , ASN A:73 , ASN A:75 , TYR A:77 , GLU A:82 , GLN A:87 , ASP A:91 , GLU A:93 , TYR A:107 , GLN A:141 , SER A:169 , TRP A:171 , HOH A:403 , HOH A:406 , HOH A:409 , HOH A:425 , HOH A:427 , HOH A:455 , HOH A:457 , HOH A:462 , HOH A:464 , HOH A:483 , HOH A:485 , HOH A:486 , HOH A:492 , HOH A:494 , HOH A:496 , HOH A:539 , HOH A:540 , HOH A:542 , HOH A:543 , HOH A:550 , HIS B:41 , GLN B:87 , ASP B:91 , GLU B:93 , GLN B:103 , ASN B:105 , TYR B:107 , GLU B:115 , ILE B:176 , ASP B:177 , ARG B:180 , TRP B:181 , GLC B:301 , XYS B:302 , HOH B:452binding site for Poly-Saccharide residues BGC A 301 through BGC A 314
2AC2SOFTWARETYR A:21 , HIS A:41 , ARG A:42 , GLY A:43 , ARG A:46 , ASN A:73 , ASN A:75 , TYR A:77 , GLU A:82 , GLN A:87 , ASP A:91 , GLU A:93 , TYR A:107 , GLN A:141 , SER A:169 , TRP A:171 , HOH A:403 , HOH A:406 , HOH A:409 , HOH A:425 , HOH A:427 , HOH A:455 , HOH A:457 , HOH A:462 , HOH A:464 , HOH A:483 , HOH A:485 , HOH A:486 , HOH A:492 , HOH A:494 , HOH A:496 , HOH A:539 , HOH A:540 , HOH A:542 , HOH A:543 , HOH A:550 , TYR B:21 , CYS B:22 , HIS B:41 , ARG B:42 , GLY B:43 , ARG B:46 , ASN B:73 , ASN B:75 , TYR B:77 , GLU B:82 , GLN B:87 , ASP B:91 , GLU B:93 , GLN B:103 , ASN B:105 , TYR B:107 , GLU B:115 , SER B:169 , TRP B:171 , ILE B:176 , ASP B:177 , ARG B:180 , TRP B:181 , HOH B:404 , HOH B:408 , HOH B:449 , HOH B:452 , HOH B:455 , HOH B:457 , HOH B:461 , HOH B:473 , HOH B:482 , HOH B:489 , HOH B:492 , HOH B:496binding site for Poly-Saccharide residues GLC B 301 through BGC B 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DZG)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:190 -Pro A:191
2Ala B:190 -Pro B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DZG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DZG)

(-) Exons   (0, 0)

(no "Exon" information available for 5DZG)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeeeehhh.ee......eeeeee.....eeeee..ee..eeeeeeee........eeeeeeee.........eeeeeee.....eeeeeee........eeee.........eeeeeee...eeeeee..eeeeeee...........eeeeeeee..hhhhhh...........eeeeeeeeee...ee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dzg A  10 EAQPLKFIAVDYCPESCTHSPESSTITLTFDHRGGSRWRSTTRFQYGTFSSLIQCPKGNTSGLNFNIYLSSLEGDKSQDAIDFEFLGKDKRIVQTNYYTAGTGNREAIHDLGFDCSDGFHEYVIKWGPDLIQWLIDGKVIRSVRADGEGFPQKPMFLYASVWDASYIDEGRWTGPYVGCDAPYICLYKNVNVPGTAV 207
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199  ||   
                                                                                                                                                                                                                          202|   
                                                                                                                                                                                                                           204   


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeeeehhh.eee.....eeeeee.....eeeee..ee..eeeeeeee........eeeeeeee.........eeeeeee.....eeeeeee........eeee.........eeeeeee...eeeeee..eeeeeee...........eeeeeeee..hhhhhh...........eeeeeeeeeee...ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5dzg B  10 EAQPLKFIAVDYCPESCTHSPESSTITLTFDHRGGSRWRSTTRFQYGTFSSLIQCPKGNTSGLNFNIYLSSLEGDKSQDAIDFEFLGKDKRIVQTNYYTAGTGNREAIHDLGFDCSDGFHEYVIKWGPDLIQWLIDGKVIRSVRADGEGFPQKPMFLYASVWDASYIDEGRWTGPYVGCDAPYICLYKNVNVPVGTAV 207
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199
   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  (0, 0)

(no "SCOP Domain" information available for 5DZG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DZG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DZG)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/TrEMBL
        F6I323_VITVI | F6I323: 5dze 5dzf 5sv8

(-) Related Entries Specified in the PDB File

5dze 5dzf