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 AN ACTIVE SITE MUTANT OF A FAMILY TWO CARBOHYDRATE ESTERASE FROM CLOSTRIDIUM THERMOCELLUM IN COMPLEX WITH CELLUOHEXASE
 
Authors :  C. Montainer, V. A. Money, V. M. R. Pires, J. E. Flint, B. A. Pinheiro, A. Goyal, J. A. M. Prates, A. Izumi, H. Stalbrand, K. Kolenova, E. Topakas, E. J. Dodson, D. N. Bolam, G. J. Davies, C. M. G. A. Fontes, H. J. Gilbert
Date :  04 Feb 09  (Deposition) - 24 Mar 09  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Plant Cell Wall Degradation, Carbohydrate Metabolism, Polysaccharide Degradation, Esterase, Hydrolase, Cellulases, Glycosidase, Carbohydrate Binding, Cellulose Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Montanier, V. A. Money, V. M. R. Pires, J. E. Flint, B. A. Pinheiro, A. Goyal, J. A. M. Prates, A. Izumi, H. Stalbrand, C. Morland, A. Cartmell, K. Kolenova, E. Topakas, E. J. Dodson, D. N. Bolam, G. J. Davies, C. M. G. A. Fontes, H. J. Gilbert
The Active Site Of A Carbohydrate Esterase Displays Divergent Catalytic And Noncatalytic Binding Functions.
Plos Biol. V. 7 E71 2009
PubMed-ID: 19338387  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1000071

(-) Compounds

Molecule 1 - ENDOGLUCANASE E
    Atcc: 27405
    Chains: A
    EC Number: 3.2.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: C TERMINAL DOMAIN CEL5C-CES2A, RESIDUES 485-814
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 1515
    Synonym: ENDO-1,4-BETA-GLUCANASE E, CARBOHYDRATE ESTERASE, CELLULASE E, EGE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric/Biological Unit (3, 17)
No.NameCountTypeFull Name
1BGC5Ligand/IonBETA-D-GLUCOSE
2GOL6Ligand/IonGLYCEROL
3IOD6Ligand/IonIODIDE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:265 , GLN A:298 , TRP A:309 , ALA A:314 , BGC A:1336 , HOH A:2351 , HOH A:2352 , HOH A:2353BINDING SITE FOR RESIDUE BGC A1335
02AC2SOFTWAREMET A:263 , SER A:302 , TRP A:309 , BGC A:1335 , BGC A:1337 , IOD A:1349 , HOH A:2354 , HOH A:2355 , HOH A:2356 , HOH A:2359BINDING SITE FOR RESIDUE BGC A1336
03AC3SOFTWAREMET A:263 , ASP A:308 , BGC A:1336 , BGC A:1338 , IOD A:1349 , HOH A:2357 , HOH A:2358 , HOH A:2359BINDING SITE FOR RESIDUE BGC A1337
04AC4SOFTWAREALA A:131 , TYR A:136 , GLY A:177 , ASP A:308 , HIS A:310 , BGC A:1337 , BGC A:1339 , HOH A:2360 , HOH A:2361 , HOH A:2362BINDING SITE FOR RESIDUE BGC A1338
05AC5SOFTWARESER A:176 , GLY A:177 , BGC A:1338 , GOL A:1342 , HOH A:2205 , HOH A:2360 , HOH A:2363 , HOH A:2364 , HOH A:2365 , HOH A:2366BINDING SITE FOR RESIDUE BGC A1339
06AC6SOFTWAREASP A:60 , PRO A:190 , ARG A:195 , TYR A:198 , PRO A:201 , GOL A:1344BINDING SITE FOR RESIDUE GOL A1340
07AC7SOFTWAREPHE A:296 , PRO A:297 , THR A:315 , LEU A:318 , IOD A:1350 , HOH A:2367BINDING SITE FOR RESIDUE GOL A1341
08AC8SOFTWARETRP A:175 , ILE A:178 , ASN A:183 , PRO A:190 , ARG A:195 , BGC A:1339 , HOH A:2368BINDING SITE FOR RESIDUE GOL A1342
09AC9SOFTWAREGLN A:56 , ASN A:153 , TYR A:155 , MET A:156 , HOH A:2173 , HOH A:2369BINDING SITE FOR RESIDUE GOL A1343
10BC1SOFTWAREASP A:60 , ALA A:86 , HIS A:87 , TYR A:198 , TYR A:202 , GLY A:204 , GOL A:1340 , HOH A:2371BINDING SITE FOR RESIDUE GOL A1344
11BC2SOFTWAREPRO A:65 , PHE A:67 , VAL A:76 , LYS A:77 , LEU A:78 , HOH A:2374 , HOH A:2375 , HOH A:2376BINDING SITE FOR RESIDUE GOL A1345
12BC3SOFTWAREGLU A:101BINDING SITE FOR RESIDUE IOD A1346
13BC4SOFTWARETYR A:13 , HOH A:2131BINDING SITE FOR RESIDUE IOD A1347
14BC5SOFTWARESER A:227 , MET A:263 , BGC A:1336 , BGC A:1337BINDING SITE FOR RESIDUE IOD A1349
15BC6SOFTWAREPRO A:297 , ARG A:322 , GOL A:1341 , HOH A:2335BINDING SITE FOR RESIDUE IOD A1350
16BC7SOFTWARETRP A:333 , HOH A:2276BINDING SITE FOR RESIDUE IOD A1351

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:261 -Pro A:262

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WAB)

(-) 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:327
 aligned with CELE_CLOTH | P10477 from UniProtKB/Swiss-Prot  Length:814

    Alignment length:327
                                                                                                                                                                                                                                                                                                                                                               814 
                                   498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808     | 
           CELE_CLOTH   489 NPGILYNGRFDFSDPNGPKCAWSGSNVELNFYGTEASVTIKSGGENWFQAIVDGNPLPPFSVNATTSTVKLVSGLAEGAHHLVLWKRTEASLGEVQFLGFDFGSGKLLAAPKPLERKIEFIGDSITCAYGNEGTSKEQSFTPKNENSYMSYAAITARNLNASANMIAWSGIGLTMNYGGAPGPLIMDRYPYTLPYSGVRWDFSKYVPQVVVINLGTNDFSTSFADKTKFVTAYKNLISEVRRNYPDAHIFCCVGPMLWGTGLDLCRSYVTEVVNDCNRSGDLKVYFVEFPQQDGSTGYGEDWHPSIATHQLMAERLTAEIKNKLGW-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..................eeeeeeee..eeeeeeeeeeeeeeeee.........................eeeeeeeee..hhhhh............ee.........eeeeeehhhhhh............hhhhhhhhhhhhhhhhhhh..eeeeee........hhhhh...hhhhhh.eee....ee.hhhhh...eeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhhhhhh....eeeee..........hhhhh.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wab A   8 NPGILYNGRFDFSDPNGPKCAWSGSNVELNFYGTEASVTIKSGGENWFQAIVDGNPLPPFSVNATTSTVKLVSGLAEGAHHLVLWKRTEASLGEVQFLGFDFGSGKLLAAPKPLERKIEFIGDAITCAYGNEGTSKEQSFTPKNENSYMSYAAITARNLNASANMIAWSGIGLTMNYGGAPGPLIMDRYPYTLPYSGVRWDFSKYVPQVVVINLGTNDFSTSFADKTKFVTAYKNLISEVRRNYPDAHIFCCVGPMLWGTGLDLCRSYVTEVVNDCNRSGDLKVYFVEFPQQDGSTGYGEDWHPSIATHQLMAERLTAEIKNKLGWL 334
                                    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       287       297       307       317       327
   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 2WAB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CELE_CLOTH | P10477)
molecular function
    GO:0046555    acetylxylan esterase activity    Catalysis of the deacetylation of xylans and xylo-oligosaccharides.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0008810    cellulase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
    GO:0030248    cellulose binding    Interacting selectively and non-covalently with cellulose.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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:2000884    glucomannan catabolic process    The chemical reactions and pathways resulting in the breakdown of a glucomannan.
    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.
    GO:0045493    xylan catabolic process    The chemical reactions and pathways resulting in the breakdown of xylan, a polymer containing a beta-1,4-linked D-xylose backbone.
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
    BGC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IOD  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:261 - Pro A:262   [ 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
  2wab
    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
  CELE_CLOTH | P10477
    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
  CELE_CLOTH | P10477
    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
        CELE_CLOTH | P10477: 2wao 4im4

(-) Related Entries Specified in the PDB File

2w9x THE ACTIVE SITE OF A CARBOHYDRATE ESTERASE DISPLAYS DIVERGENT CATALYTIC AND NON-CATALYTIC BINDING FUNCTIONS
2waa STRUCTURE OF A FAMILY TWO CARBOHYDRATE ESTERASE FROM CELLVIBRIO JAPONICUS
2wao STRUCTURE OF A FAMILY TWO CARBOHYDRATE ESTERASE FROM CLOSTRIDIUM THERMOCELLUM IN COMPLEX WITH CELLOHEXAOSE