Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A FAMILY 26 LICHENASE IN COMPLEX WITH NOEUROMYCIN
 
Authors :  P. J. Meloncelli, T. M. Gloster, V. A. Money, C. A. Tarling, G. J. Davies, S. G. Withers, R. V. Stick
Date :  18 Jun 07  (Deposition) - 18 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-1 4 Beta-1 3 Glucanase, Lichenase, Hydrolase, Glycosidase, Glycoside Hydrolase Family 26, Polysaccharide Degradation, Cellulose Degradation, Carbohydrate Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Meloncelli, T. M. Gloster, V. A. Money, C. A. Tarling, G. J. Davies, S. G. Withers, R. V. Stick
D-Glucosylated Derivatives Of Isofagomine And Noeuromycin And Their Potential As Inhibitors Of Beta-Glycoside Hydrolases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENDOGLUCANASE H
    Atcc: 27405
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCF1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET21A
    Fragment: CATALYTIC DOMAIN, RESIDUES 26-305
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Strain: F1/YS
    Synonym: EGH, ENDO-1,4-BETA-GLUCANASE H, CELLULASE H, LICHENASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2NOY1Ligand/Ion(2R,3S,4R,5R)-5-(HYDROXYMETHYL)PIPERIDINE-2,3,4-TRIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:14 , PHE A:41 , GLU A:70 , TYR A:115 , PHE A:256 , GLU A:258 , LYS A:260 , NOY A:1282 , HOH A:2064 , HOH A:2449 , HOH A:2483 , HOH A:2484 , HOH A:2485BINDING SITE FOR RESIDUE BGC A1281
2AC2SOFTWAREHIS A:108 , GLU A:109 , TYR A:115 , TYR A:185 , TRP A:187 , GLU A:222 , PHE A:256 , LYS A:260 , GLU A:261 , BGC A:1281 , HOH A:2488BINDING SITE FOR RESIDUE NOY A1282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V3G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2V3G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V3G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V3G)

(-) Exons   (0, 0)

(no "Exon" information available for 2V3G)

(-) 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:273
 aligned with GUNH_CLOTH | P16218 from UniProtKB/Swiss-Prot  Length:900

    Alignment length:273
                                    39        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   
           GUNH_CLOTH    30 GLKIGAWVGTQPSESAIKSFQELQGRKLDIVHQFINWSTDFSWVRPYADAVYNNGSILMITWEPWEYNTVDIKNGKADAYITRMAQDMKAYGKEIWLRPLHEANGDWYPWAIGYSSRVNTNETYIAAFRHIVDIFRANGATNVKWVFNVNCDNVGNGTSYLGHYPGDNYVDYTSIDGYNWGTTQSWGSQWQSFDQVFSRAYQALASINKPIIIAEFASAEIGGNKARWITEAYNSIRTSYNKVIAAVWFHENKETDWRINSSPEALAAYREAI 302
               SCOP domains d2v3ga_ A: automated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------Glyco_hydro_26-2v3gA01 A:48-265                                                                                                                                                                                           --------------- Pfam domains
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh..eeeeeee....hhhhhhh..hhhhhhhhhhhhhhhh..eeeee....................hhhhhhhhhhhhhhhhhhh....eee...ee...............hhhhh..eeeeeee............hhhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v3g A   8 GLKIGAWVGTQPSESAIKSFQELQGRKLDIVHQFINWSTDFSWVRPYADAVYNNGSILMITWEPWEYNTVDIKNGKADAYITRMAQDMKAYGKEIWLRPLHEANGDWYPWAIGYSSRVNTNETYIAAFRHIVDIFRANGATNVKWVFNVNCDNVGNGTSYLGHYPGDNYVDYTSIDGYNWGTTQSWGSQWQSFDQVFSRAYQALASINKPIIIAEFASAEIGGNKARWITEAYNSIRTSYNKVIAAVWFHENKETDWRINSSPEALAAYREAI 280
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V3G)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUNH_CLOTH | P16218)
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.
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:0030245    cellulose catabolic process    The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NOY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2v3g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2v3g
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GUNH_CLOTH | P16218
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.1.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GUNH_CLOTH | P16218
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        GUNH_CLOTH | P16218: 1v0a 2bv9 2bvd 2cip 2cit 2lro 2lrp 2vi0 4u3a 4u5i 4u5k 5byw

(-) Related Entries Specified in the PDB File

1v0a FAMILY 11 CARBOHYDRATE-BINDING MODULE OF CELLULOSOMAL CELLULASE LIC26A-CEL5E OF CLOSTRIDIUM THERMOCELLUM
2bv9 HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CTLIC26A
2bvd HOW FAMILY 26 GLYCOSIDE HYDROLASES ORCHESTRATE CATALYSIS ON DIFFERENT POLYSACCHARIDES. STRUCTURE AND ACTIVITY OF A CLOSTRIDIUM THERMOCELLUM LICHENASE, CTLIC26A
2cip STRUCTURE OF THE MICHAELIS COMPLEX OF A FAMILY 26 LICHENASE
2cit STRUCTURE OF THE COVALENT INTERMEDIATE OF A FAMILY 26 LICHENASE