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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EXTRACELLULAR XYLANASE FROM GEOBACILLUS STEAROTHERMOPHILUS T-6 (XT6, MONOCLINIC FORM): THE E159A/E265A MUTANT AT 1.8A RESOLUTION
 
Authors :  M. Bar, G. Golan, G. Zolotnitsky, Y. Shoham, G. Shoham
Date :  23 Oct 03  (Deposition) - 19 Jul 05  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bar, G. Golan, G. Zolotnitsky, Y. Shoham, G. Shoham
Crystal Structure Of The Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (Xt6, Monoclinic Form): The E159A/E265A Mutant At 1. 8A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET9D
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: XYNA
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
    Synonym: XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE, XYLANASE T-6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
3ZN7Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:11 , GLU A:27 , ASP A:365 , CL A:701BINDING SITE FOR RESIDUE ZN A 901
02AC2SOFTWAREASP A:21 , HOH A:1001 , HOH A:1162 , HOH A:1163 , HOH A:1164 , HOH A:1165BINDING SITE FOR RESIDUE ZN A 902
03AC3SOFTWAREASP A:282 , HIS A:378 , HOH A:1232 , HOH A:1298 , HOH A:1299BINDING SITE FOR RESIDUE ZN A 903
04AC4SOFTWAREASP A:282 , HIS A:378 , HOH A:1274 , HOH A:1303 , HOH A:1347BINDING SITE FOR RESIDUE ZN A 904
05AC5SOFTWAREGLU A:58 , HIS A:322 , CL A:702 , HOH A:1099BINDING SITE FOR RESIDUE ZN A 905
06AC6SOFTWAREGLU A:27 , SER A:307 , ILE A:310 , HOH A:1066 , HOH A:1231 , HOH A:1233BINDING SITE FOR RESIDUE ZN A 906
07AC7SOFTWAREASP A:297 , ALA A:374 , ASP A:377 , LYS A:379 , HOH A:1018 , HOH A:1297 , HOH A:1331BINDING SITE FOR RESIDUE ZN A 907
08AC8SOFTWAREHIS A:11 , ASN A:26 , GLU A:27 , ASP A:365 , ZN A:901 , HOH A:1274BINDING SITE FOR RESIDUE CL A 701
09AC9SOFTWAREGLU A:58 , HIS A:322 , TRP A:324 , ZN A:905 , HOH A:1071BINDING SITE FOR RESIDUE CL A 702
10BC1SOFTWAREASP A:377 , HIS A:378 , LYS A:379BINDING SITE FOR RESIDUE SO4 A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R86)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:95 -Thr A:96
2Glu A:208 -Pro A:209
3Trp A:241 -Pro A:242
4Trp A:273 -Pro A:274

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R86)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_2PS51760 Glycosyl hydrolases family 10 (GH10) domain profile.XYN1_GEOSE42-406  1A:14-378
2GH10_1PS00591 Glycosyl hydrolases family 10 (GH10) active site.XYN1_GEOSE286-296  1A:258-268

(-) Exons   (0, 0)

(no "Exon" information available for 1R86)

(-) 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:371
 aligned with XYN1_GEOSE | P40943 from UniProtKB/Swiss-Prot  Length:407

    Alignment length:371
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406 
           XYN1_GEOSE    37 KPHISALNAPQLDQRYKNEFTIGAAVEPYQLQNEKDVQMLKRHFNSIVAENVMKPISIQPEEGKFNFEQADRIVKFAKANGMDIRFHTLVWHSQVPQWFFLDKEGKPMVNETDPVKREQNKQLLLKRLETHIKTIVERYKDDIKYWDVVNEVVGDDGKLRNSPWYQIAGIDYIKVAFQAARKYGGDNIKLYMNDYNTEVEPKRTALYNLVKQLKEEGVPIDGIGHQSHIQIGWPSEAEIEKTINMFAALGLDNQITELDVSMYGWPPRAYPTYDAIPKQKFLDQAARYDRLFKLYEKLSDKISNVTFWGIADNHTWLDSRADVYYDANGNVVVDPNAPYAKVEKGKGKDAPFVFGPDYKVKPAYWAIIDHK 407
               SCOP domains d1r86a1 A:9-379 Xylanase                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1r86A00 A:9-379 Glycosidases                                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------Glyco_hydro_10-1r86A01 A:19-379                                                                                                                                                                                                                                                                                                                                           Pfam domains
         Sec.struct. author ....hhhhh.hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhh.....eeee..eee....hhhhhhhhhhhhhhh..eeeeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhh.eee.....ee........eee.................hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----GH10_2  PDB: A:14-378 UniProt: 42-406                                                                                                                                                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     --------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r86 A   9 KPHISALNAPQLDQRYKNEFTIGAAVEPYQLQNEKDVQMLKRHFNSIVAENVMKPISIQPEEGKFNFEQADRIVKFAKANGMDIRFHTLVWHSQVPQWFFLDKEGKPMVNETDPVKREQNKQLLLKRLETHIKTIVERYKDDIKYWDVVNAVVGDDGKLRNSPWYQIAGIDYIKVAFQAARKYGGDNIKLYMNDYNTEVEPKRTALYNLVKQLKEEGVPIDGIGHQSHIQIGWPSEAEIEKTINMFAALGLDNQITALDVSMYGWPPRAYPTYDAIPKQKFLDQAARYDRLFKLYEKLSDKISNVTFWGIADNHTWLDSRADVYYDANGNVVVDPNAPYAKVEKGKGKDAPFVFGPDYKVKPAYWAIIDHK 379
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
   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  (1, 1)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYN1_GEOSE | P40943)
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.
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.

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  1r86
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  XYN1_GEOSE | P40943
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 Related Entries

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

UniProtKB/Swiss-Prot
        XYN1_GEOSE | P40943: 1hiz 1r85 1r87 3mmd 4prw 4pud 4pue

(-) Related Entries Specified in the PDB File

1r85 1r87