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(-) Description

Title :  XYLANASE II FROM TRICHODERMA REESEI COCRYSTALLIZED WITH TRIS-DIPICOLINATE EUROPIUM
 
Authors :  G. Pompidor, R. Kahn, O. Maury
Date :  21 Jan 10  (Deposition) - 19 Jan 11  (Release) - 19 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Europium Tris-Dipicolinate Complex, Glycoprotein, Glycosidase, Hydrolase, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Pompidor, O. Maury, J. Vicat, R. Kahn
A Dipicolinate Lanthanide Complex For Solving Protein Structures Using Anomalous Diffraction.
Acta Crystallogr. , Sect. D V. 66 762 2010
PubMed-ID: 20606256  |  Reference-DOI: 10.1107/S0907444910010954

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE 2
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: TRICHODERMA LONGIBRACHIATUM
    Expression System Taxid: 5548
    Gene: XYN2
    Organism Common: HYPOCREA JECORINA
    Organism Scientific: HYPOCREA JECORINA
    Organism Taxid: 51453
    Synonym: XYLANASE 2, 1,4-BETA-D-XYLAN XYLANOHYDROLASE 2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1EU3Ligand/IonEUROPIUM ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3PDC3Ligand/IonPYRIDINE-2,6-DICARBOXYLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPDC A:302 , PDC A:303 , PDC A:304BINDING SITE FOR RESIDUE EU A 201
2AC2SOFTWAREHOH A:229BINDING SITE FOR RESIDUE EU A 202
3AC3SOFTWAREHOH A:331 , HOH A:544BINDING SITE FOR RESIDUE EU A 203
4AC4SOFTWAREGLN A:4 , PRO A:5 , ASN A:19 , GLY A:21 , HIS A:22 , GLY A:23 , GLY A:24 , EU A:201 , PDC A:303 , PDC A:304 , HOH A:383 , HOH A:514BINDING SITE FOR RESIDUE PDC A 302
5AC5SOFTWAREGLN A:4 , PRO A:5 , ASN A:19 , GLY A:21 , HIS A:22 , GLY A:23 , GLY A:24 , EU A:201 , PDC A:302 , PDC A:304 , HOH A:383 , HOH A:514BINDING SITE FOR RESIDUE PDC A 303
6AC6SOFTWAREILE A:3 , GLN A:4 , TYR A:17 , VAL A:25 , EU A:201 , PDC A:302 , PDC A:303 , HOH A:351 , HOH A:395BINDING SITE FOR RESIDUE PDC A 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LGR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:52 -Pro A:53
2Asn A:82 -Pro A:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_3PS51761 Glycosyl hydrolases family 11 (GH11) domain profile.XYN2_HYPJR34-223  1A:2-190
2GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYN2_HYPJR116-126  1A:83-93
3GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYN2_HYPJR207-218  1A:174-185

(-) Exons   (0, 0)

(no "Exon" information available for 3LGR)

(-) 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:190
 aligned with XYN2_HYPJR | P36217 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:190
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
           XYN2_HYPJR    34 QTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 223
               SCOP domains d3lgra_ A: Xylanase II                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeeee...eeeeeeeee.........eeeeeeee..eeeeeeeeeeeee......eeeeeeeeee......eeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GH11_3  PDB: A:2-190 UniProt: 34-223                                                                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lgr A   1 xTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
                            |                                                                                                                                                                                             
                            1-PCA
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  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: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYN2_HYPJR | P36217)
molecular function
    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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  3lgr
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  XYN2_HYPJR | P36217
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYN2_HYPJR | P36217: 1enx 1red 1ree 1ref 1xyo 1xyp 2d97 2d98 2dfb 2dfc 4hk8 4hk9 4hkl 4hko 4hkw 4s2d 4s2f 4s2g 4s2h 4xpv 4xq4 4xqd 4xqw 5k7p

(-) Related Entries Specified in the PDB File

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