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(-) Description

Title :  CRYSTAL STRUCTURE OF XEG-EDGP
 
Authors :  T. Yoshizawa, T. Shimizu, H. Hirano, M. Sato, H. Hashimoto
Date :  30 Nov 11  (Deposition) - 18 Apr 12  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cell-Wall, Plant Protein-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yoshizawa, T. Shimizu, H. Hirano, M. Sato, H. Hashimoto
Structural Basis For Inhibition Of Xyloglucan-Specific Endo-Beta-1, 4-Glucanase (Xeg) By Xeg-Protein Inhibitor
J. Biol. Chem. V. 287 18710 2012
PubMed-ID: 22496365  |  Reference-DOI: 10.1074/JBC.M112.350520

(-) Compounds

Molecule 1 - EDGP
    Chains: A, C
    Engineered: YES
    Expression System: DAUCUS CAROTA
    Expression System Cell: CARROT CALLUS CELL
    Expression System Common: CARROT
    Expression System Taxid: 4039
    Gene: EDGP1
    Organism Common: CARROT
    Organism Scientific: DAUCUS CAROTA
    Organism Taxid: 4039
 
Molecule 2 - XYLOGLUCAN-SPECIFIC ENDO-BETA-1,4-GLUCANASE A
    Chains: B, D
    EC Number: 3.2.1.151
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 21-238
    Gene: XGEA
    Organism Scientific: ASPERGILLUS ACULEATUS
    Organism Taxid: 5053
    Synonym: XYLOGLUCANASE A, XYLOGLUCANENDOHYDROLASE A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3VLB)

(-) Sites  (0, 0)

(no "Site" information available for 3VLB)

(-) SS Bonds  (14, 14)

Asymmetric Unit
No.Residues
1A:50 -A:138
2A:64 -A:77
3A:69 -A:93
4A:80 -A:88
5A:181 -A:406
6A:312 -A:358
7B:10 -B:38
8C:50 -C:138
9C:64 -C:77
10C:69 -C:93
11C:80 -C:88
12C:181 -C:406
13C:312 -C:358
14D:10 -D:38

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Thr A:30 -Pro A:31
2Asp A:197 -Pro A:198
3Leu A:202 -Pro A:203
4Ala A:307 -Pro A:308
5Thr C:30 -Pro C:31
6Asp C:197 -Pro C:198
7Leu C:202 -Pro C:203
8Ala C:307 -Pro C:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VLB)

(-) 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:404
 aligned with Q05929_DAUCA | Q05929 from UniProtKB/TrEMBL  Length:433

    Alignment length:408
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
         Q05929_DAUCA    25 RPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCFNGPRPGCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSATSTQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFT 432
               SCOP domains d3vlba_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeee....eeeeeeee......eee..........ee....hhhhhhhh.....ee...---.ee....ee..eehhhhee..eeeeeeeeeeeee....eeeeeeeeeeeeeeehhhhhh.......eeee......hhhhhhhhhhh...eeeee........eeeeee...eee...eee.....eeeeee.........-........eee...eeee.......hhhhhh........eee......eeehhhhhhhhhhhhhhhhhhh.............eee.....ee..ee....eeee......eeeehhhhheee....eeee.eee........eee.......eeeeee....eeeeeee.hhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vlb A   5 RPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCFNG---GCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSAT-TQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFT 412
                                    14        24        34        44        54        64        74        |-  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224  | |  234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404        
                                                                                                         83  87                                                                                                                                         227 |                                                                                                                                                                                       
                                                                                                                                                                                                                                                          229                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with XGEA_ASPAC | O94218 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:218
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           XGEA_ASPAC    21 SDFCGQWDTATAGDFTLYNDLWGESAGTGSQCTGVDSYSGDTIAWHTSWSWSGGSSSVKSYVNAALTFTPTQLNCISSIPTTWKWSYSGSSIVADVAYDTFLAETASGSSKYEIMVWLAALGGAGPISSTGSTIATPTIAGVNWKLYSGPNGDTTVYSFVADSTTESFSGDLNDFFTYLVDNEGVSDELYLTTLEAGTEPFTGSNAKLTVSEYSISIE 238
               SCOP domains d3vlbb_ B: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee..eeee....hhhhheeeeeeeeeeee..eeeeeeeeeee.........eeeee....ee.hhh...eeeeeeeeeeeeeeeeeeeeeeee........eeeeeeeeee................ee..eeeeeeeee....eeeeeee.....eeeeehhhhhhhhhhhh......eeeeeeeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlb B   7 SDFCGQWDTATAGDFTLYNDLWGESAGTGSQCTGVDSYSGDTIAWHTSWSWSGGSSSVKSYVNAALTFTPTQLNCISSIPTTWKWSYSGSSIVADVAYDTFLAETASGSSKYEIMVWLAALGGAGPISSTGSTIATPTIAGVNWKLYSGPNGDTTVYSFVADSTTESFSGDLNDFFTYLVDNEGVSDELYLTTLEAGTEPFTGSNAKLTVSEYSISIE 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        


Chain C from PDB  Type:PROTEIN  Length:403
 aligned with Q05929_DAUCA | Q05929 from UniProtKB/TrEMBL  Length:433

    Alignment length:408
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424        
         Q05929_DAUCA    25 RPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCFNGPRPGCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSATSTQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFT 432
               SCOP domains d3vlbc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee......eeeeeee....eeeeeeee......eee..........ee....hhhhhh..........-----...........ee....ee....eeeeeeeeeee....eeeeeeeeeeeeeeehhhhhh.......eeee......hhhhhhhhhhh...eeeee........eeeeee...eee...eee.....eeeeee..................eee...eeee.....................eee......eee.hhhhhhhhhhhhhhhhh....ee........eee.....ee..ee....eeee......eeeehhhhheee....eeee.eee........eee.hhhhh.eeeeee....eeeeeee......hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vlb C   5 RPSALVVPVKKDASTLQYVTTINQRTPLVSENLVVDLGGRFLWVDCDQNYVSSTYRPVRCRTSQCSLSGSIACGDCF-----GCNNNTCGVFPENPVINTATGGEVAEDVVSVESTDGSSSGRVVTVPRFIFSCAPTSLLQNLASGVVGMAGLGRTRIALPSQFASAFSFKRKFAMCLSGSTSSNSVIIFGNDPYTFLPNIIVSDKTLTYTPLLTNPVSTSATSTQGEPSVEYFIGVKSIKINSKIVALNTSLLSISSAGLGGTKISTINPYTVLETSIYKAVTEAFIKESAARNITRVASVAPFGACFSTDNILSTRLGPSVPSIDLVLQSESVVWTITGSNSMVYINDNVVCLGVVDGGSNLRTSIVIGGHQLEDNLVQFDLATSRVGFSGTLLGSRTTCANFNFT 412
                                    14        24        34        44        54        64        74      |  -  |     94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404        
                                                                                                       81    87                                                                                                                                                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with XGEA_ASPAC | O94218 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:218
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           XGEA_ASPAC    21 SDFCGQWDTATAGDFTLYNDLWGESAGTGSQCTGVDSYSGDTIAWHTSWSWSGGSSSVKSYVNAALTFTPTQLNCISSIPTTWKWSYSGSSIVADVAYDTFLAETASGSSKYEIMVWLAALGGAGPISSTGSTIATPTIAGVNWKLYSGPNGDTTVYSFVADSTTESFSGDLNDFFTYLVDNEGVSDELYLTTLEAGTEPFTGSNAKLTVSEYSISIE 238
               SCOP domains d3vlbd_ D: automated matches                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee..eeee....hhhhheeeeeeeeeeee..eeeeeeeeeee.........eeeee....ee.hhh...eeeeeeeeeeeeeeeeeeeeeeee......eeeeeeeeeeee................ee..eeeeeeeeee..eeeeeeee.....eeeeehhhhhhhhhhhh......eeeeeeeeeeeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlb D   7 SDFCGQWDTATAGDFTLYNDLWGESAGTGSQCTGVDSYSGDTIAWHTSWSWSGGSSSVKSYVNAALTFTPTQLNCISSIPTTWKWSYSGSSIVADVAYDTFLAETASGSSKYEIMVWLAALGGAGPISSTGSTIATPTIAGVNWKLYSGPNGDTTVYSFVADSTTESFSGDLNDFFTYLVDNEGVSDELYLTTLEAGTEPFTGSNAKLTVSEYSISIE 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q05929_DAUCA | Q05929)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain B,D   (XGEA_ASPAC | O94218)
molecular function
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal 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.
    GO:0033946    xyloglucan-specific endo-beta-1,4-glucanase activity    Catalysis of the reaction: xyloglucan + H2O = xyloglucan oligosaccharides. This reaction is the endohydrolysis of (1->4)-beta-D-glucosidic linkages in xyloglucan.
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.
    GO:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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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    Ala A:307 - Pro A:308   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        XGEA_ASPAC | O94218: 3vl8 3vl9
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(-) Related Entries Specified in the PDB File

3vl8 3vl9 3vla