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(-) Description

Title :  CRYSTAL STRUCTURE OF LOOP SWAP MUTANT OF NECALLIMASTIX PATRICIARUM XYN11A
 
Authors :  M. Vardakou, C. Dumon, J. E. Flint, J. W. Murray, P. Christakopoulos, D. P. Weiner, N. Juge, R. J. Lewis, H. J. Gilbert
Date :  09 Nov 07  (Deposition) - 25 Dec 07  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Xylanase, Hydrolase, Glycosidase, Beta Jelly Roll, Multifunctional Enzyme, Xylan Degradation, Glycoside Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Vardakou, C. Dumon, J. W. Murray, P. Christakopoulos, D. P. Weiner, N. Juge, R. J. Lewis, H. J. Gilbert, J. E. Flint
Understanding The Structural Basis For Substrate And Inhibitor Recognition In Eukaryotic Gh11 Xylanases.
J. Mol. Biol. V. 375 1293 2008
PubMed-ID: 18078955  |  Reference-DOI: 10.1016/J.JMB.2007.11.007

(-) Compounds

Molecule 1 - BIFUNCTIONAL ENDO-1,4-BETA-XYLANASE A
    ChainsA
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 275-297,305-492
    MutationYES
    Organism CommonRUMEN FUNGUS
    Organism ScientificNEOCALLIMASTIX PATRICIARUM
    Organism Taxid4758
    SynonymXYLA, GH11 XYLANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CD1Ligand/IonCADMIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:17 , ASP A:120 , HOH A:2064 , HOH A:2123BINDING SITE FOR RESIDUE CD A1218
2AC2SOFTWAREGLY A:35 , THR A:39 , ASP A:208 , VAL A:209BINDING SITE FOR RESIDUE ACT A1219
3AC3SOFTWAREASN A:90 , TRP A:201 , HOH A:2133 , HOH A:2265BINDING SITE FOR RESIDUE ACT A1220

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2VG9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2VG9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2VG9)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_3PS51761 Glycosyl hydrolases family 11 (GH11) domain profile.XYNA_NEOPA35-242
280-487
  1-
A:7-212
2GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_NEOPA138-148
383-393
  1-
A:108-118
3GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_NEOPA226-237
471-482
  1-
A:196-207

(-) Exons   (0, 0)

(no "Exon" information available for 2VG9)

(-) 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:217
 aligned with XYNA_NEOPA | P29127 from UniProtKB/Swiss-Prot  Length:607

    Alignment length:219
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483         
           XYNA_NEOPA   274 KKFTVGNGQNQHKGVNDGFSYEIWLDNTGGNGSMTLGSGATFKAEWNAAVNRGNFLARRGLDFGSQKKATDYDYIGLDYAATYKQTASASGNSRLCVYGWFQNRGLNGVPLVEYYIIEDWVDWVPDAQGKMVTIDGAQYKIFQMDHTGPTINGGSETFKQYFSVRQQKRTSGHITVSDHFKEWAKQGWGIGNLYEVALNAEGWQSSGVADVTLLDVYTT 492
               SCOP domains d2vg9a_ A: automated match  es                                                                                                                                                                                              SCOP domains
               CATH domains 2vg9A00 A:1-217  [code=2.6  0.120.180, no name defined]                                                                                                                                                                     CATH domains
               Pfam domains -------------Glyco_hydro_1--1-2vg9A01 A:14-211                                                                                                                                                                       ------ Pfam domains
         Sec.struct. author .eeee.....eeeeee..eeeeeeee--..eeeeee.....eeeeee......eeeeeeeee......hhhh.eeeeeeeeeeeeeeeeeeeeeeeeeeeee.........eeeeeeeeee........eeeee..eeeeeeeeeeeeee..eeeeeeeeeeeee.....eeeeehhhhhhhhhh.........eeeeeeeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------GH11_3  PDB: A:7-212 UniProt: 280-487                                                                                                                                                                           ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------GH11_2      ---------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vg9 A   1 MKFTVGNGQNQHKGVNDGFSYEIWTN--GGEGSMTLGSGATFKAEWNAAVNRGNFLARRGLDFGSQKKATDYDYIGLDYAATYKQTASASGNSRLCVYGWFQNRGLNGVPLVEYYIIEDWVDWVPDAQGKMVTIDGAQYKIFQMDHTGPTINGGSETFKQYFSVRQQKRTSGHITVSDHFKEWAKQGWGIGNLYEVALNAEGWQSSGVADVTLLDVYTT 217
                                    10        20     |  28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208         
                                                    26 27                                                                                                                                                                                              

   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

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_NEOPA | P29127)
molecular function
    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:0031176    endo-1,4-beta-xylanase activity    Catalysis of the endohydrolysis of (1->4)-beta-D-xylosidic linkages in xylans.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_NEOPA | P291272c1f

(-) Related Entries Specified in the PDB File

2c1f THE STRUCTURE OF THE FAMILY 11 XYLANASE FROM NEOCALLIMASTIX PATRICIARUM