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 :  FAMILY 5 ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOBIO-DERIVED NOEUROMYCIN
 
Authors :  T. M. Gloster, P. J. Meloncelli, V. A. Money, C. A. Tarling, G. J. Davies, S. G. Withers, R. V. Stick
Date :  13 Jun 07  (Deposition) - 26 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Endoglucanase, Glycoside Hydrolase, Polysaccharide Degradation, Family 5, Hydrolase, Noeuromycin, Glycosidase, 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 5A
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: THERMAMYL-AMYLASE PROMOT
    Expression System Strain: PL2306
    Expression System Taxid: 1423
    Expression System Vector: PMOL995
    Fragment: RESIDUES 27-331
    Organism Scientific: BACILLUS AGARADHAERENS
    Organism Taxid: 76935
    Synonym: ENDO-1,4-BETA-GLUCANASE 5A, ALKALINE CELLULASE, ENDOGLUCANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2IDR1Ligand/IonL-IDURONIC ACID
3IFL1Ligand/Ion(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:80 , LYS A:83 , GLU A:84 , GLU A:87 , LYS A:152 , GLU A:156 , GLN A:189 , HOH A:2144 , HOH A:2268 , HOH A:2400BINDING SITE FOR RESIDUE GOL A1305
2AC2SOFTWARETHR A:146 , TRP A:147 , GLY A:148 , ASN A:149 , ASN A:188 , HOH A:2257 , HOH A:2401BINDING SITE FOR RESIDUE GOL A1306
3AC3SOFTWAREGLU A:22 , ARG A:23 , GLU A:139 , TRP A:178 , ALA A:234 , IFL A:1309 , HOH A:2402 , HOH A:2403 , HOH A:2404 , HOH A:2405BINDING SITE FOR RESIDUE GOL A1307
4AC4SOFTWARELYS A:50 , ARG A:53 , HOH A:2406BINDING SITE FOR RESIDUE SO4 A1308
5AC5SOFTWARETYR A:66 , HIS A:101 , LEU A:103 , ASN A:138 , GLU A:139 , TYR A:202 , GLU A:228 , ALA A:234 , THR A:235 , GLY A:236 , TRP A:262 , GOL A:1307 , IDR A:1310 , HOH A:2403 , HOH A:2407BINDING SITE FOR RESIDUE IFL A1309
6AC6SOFTWAREHIS A:35 , TRP A:39 , TYR A:66 , TRP A:262 , LYS A:267 , GLU A:269 , IFL A:1309 , HOH A:2408 , HOH A:2409BINDING SITE FOR RESIDUE IDR A1310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V38)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:262 -Ser A:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V38)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLYCOSYL_HYDROL_F5PS00659 Glycosyl hydrolases family 5 signature.GUN5_BACAG158-167  1A:132-141

(-) Exons   (0, 0)

(no "Exon" information available for 2V38)

(-) 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:301
 aligned with GUN5_BACAG | O85465 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:301
                                    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       309       319       329 
           GUN5_BACAG    30 SVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRESA 330
               SCOP domains d2v38a_ A: automated matches                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2v38A00 A:4-304 Glycosidases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eee..eee.........eeeee.hhhhhhhhhhhhhhhhhhhh....eeeeeee........hhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhhhhhhh....eeee..............hhhhhhhhhhhhhhh......eee.hhhhhhhhhhhhh.......eeeeeeee....hhhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhhhh...eeeeee....................hhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_H------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v38 A   4 SVVEEHGQLSISNGELVNERGEQVQLKGMSSHGLQWYGQFVNYESMKWLRDDWGINVFRAAMYTSSGGYIDDPSVKEKVKEAVEAAIDLDIYVIIDWHILSDNDPNIYKEEAKDFFDEMSELYGDYPNVIYEIANEPNGSDVTWGNQIKPYAEEVIPIIRNNDPNNIIIVGTGTWSQDVHHAADNQLADPNVMYAFHFYAGTHGQNLRDQVDYALDQGAAIFVSEWGTSAATGDGGVFLDEAQVWIDFMDERNLSWANWSLTHKDESSAALMPGANPTGGWTEAELSPSGTFVREKIRESA 304
                                    13        23        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
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2V38)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GUN5_BACAG | O85465)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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.
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.

 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IDR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IFL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:262 - Ser A:263   [ RasMol ]  
 

(-) 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
  2v38
    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
  GUN5_BACAG | O85465
    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
  GUN5_BACAG | O85465
    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
        GUN5_BACAG | O85465: 1a3h 1e5j 1h11 1h2j 1h5v 1hf6 1ocq 1qhz 1qi0 1qi2 1w3k 1w3l 2a3h 3a3h 4a3h 5a3h 6a3h 7a3h 8a3h

(-) Related Entries Specified in the PDB File

1a3h ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6A RESOLUTION
1h11 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION
1h2j ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH UNHYDROLYSED AND COVALENTLY LINKED 2,4-DINITROPHENYL-2-DEOXY-2FLUORO- CELLOBIOSIDE AT 1.15 A RESOLUTION
1h5v THIOPENTASACCHARIDE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHARENS AT 1.1 A RESOLUTION IN THE TETRAGONAL CRYSTAL FORM
1hf6 ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN THE ORTHORHOMBIC CRYSTAL FORM IN COMPLEX WITH CELLOTRIOSE
1ocq COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.08 ANGSTROM RESOLUTION WITH CELLOBIO-DERIVED ISOFAGOMINE
1w3k ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOBIO DERIVED- TETRAHYDROOXAZINE
1w3l ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHAERENS IN COMPLEX WITH CELLOTRI DERIVED- TETRAHYDROOXAZINE
2a3h CELLOBIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 2.0 A RESOLUTION
3a3h CELLOTRIOSE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHERANS AT 1.6 A RESOLUTION
5a3h 2-DEOXY-2-FLURO-B-D-CELLOBIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.8 ANGSTROMS RESOLUTION
6a3h 2-DEOXY-2-FLURO-B-D-CELLOTRIOSYL/ENZYME INTERMEDIATE COMPLEX OF THE ENDOGLUCANASE CEL5A FROM BACILLUS AGARADHEARANS AT 1.6 ANGSTROM RESOLUTION
7a3h NATIVE ENDOGLUCANASE CEL5A CATALYTIC CORE DOMAIN AT 0.95 ANGSTROMS RESOLUTION