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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCING-END-XYLOSE RELEASING EXO-OLIGOXYLANASE D263G MUTANT
 
Authors :  S. Fushinobu, M. Hidaka, Y. Honda, T. Wakagi, H. Shoun, M. Kitaoka
Date :  12 Jun 06  (Deposition) - 27 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  (Alpla/Alpha)6 Barrel, Glycoside Hydrolase Family 8, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hidaka, S. Fushinobu, Y. Honda, T. Wakagi, H. Shoun, M. Kitaoka
Structural Explanation For The Acquisition Of Glycosynthase Activity
J. Biochem. 2009
PubMed-ID: 19819900  |  Reference-DOI: 10.1093/JB/MVP159
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLANASE Y
    Chains: A
    EC Number: 3.2.1.156
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B-BH2105
    Expression System Strain: BL21-GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BH2105
    Mutation: YES
    Organism Scientific: BACILLUS HALODURANS
    Organism Taxid: 272558
    Strain: C-125
    Synonym: REDUCING-END-XYLOSE RELEASING EXO-OLIGOXYLANASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:27 , GLU A:30 , ASP A:253 , HIS A:259BINDING SITE FOR RESIDUE NI A 1400
2AC2SOFTWARETRP A:123 , GLU A:192 , TYR A:246 , TYR A:247 , ASP A:248 , HOH A:1571BINDING SITE FOR RESIDUE GOL A 1401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:150 -Pro A:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DRQ)

(-) 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:377
 aligned with REOX_BACHD | Q9KB30 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:379
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
           REOX_BACHD     3 KTTEGAFYTREYRNLFKEFGYSEAEIQERVKDTWEQLFGDNPETKIYYEVGDDLGYLLDTGNLDVRTEGMSYGMMMAVQMDRKDIFDRIWNWTMKNMYMTEGVHAGYFAWSCQPDGTKNSWGPAPDGEEYFALALFFASHRWGDGDEQPFNYSEQARKLLHTCVHNGEGGPGHPMWNRDNKLIKFIPEVEFSDPSYHLPHFYELFSLWANEEDRVFWKEAAEASREYLKIACHPETGLAPEYAYYDGTPNDEKGYGHFFSDSYRVAANIGLDAEWFGGSEWSAEEINKIQAFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPYAKANVDLFWNTPVRTGNRRYYDNCLYLFAMLALSGNFKIWFP 381
               SCOP domains d2drqa_ A: Xylanase Y                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhh...--..eeee...eeee.......eehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.............ee...........hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........................eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........ee..............hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhh.eee.....eeeee..hhhhhhhhhhhhhhhh....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2drq A   3 KTTEGAFYTREYRNLFKEFGYSEAEIQERVKDTWEQLFGDNP--KIYYEVGDDLGYLLDTGNLDVRTEGMSYGMMMAVQMDRKDIFDRIWNWTMKNMYMTEGVHAGYFAWSCQPDGTKNSWGPAPDGEEYFALALFFASHRWGDGDEQPFNYSEQARKLLHTCVHNGEGGPGHPMWNRDNKLIKFIPEVEFSDPSYHLPHFYELFSLWANEEDRVFWKEAAEASREYLKIACHPETGLAPEYAYYDGTPNDEKGYGHFFSGSYRVAANIGLDAEWFGGSEWSAEEINKIQAFFADKEPEDYRRYKIDGEPFEEKSLHPVGLIATNAMGSLASVDGPYAKANVDLFWNTPVRTGNRRYYDNCLYLFAMLALSGNFKIWFP 381
                                    12        22        32        42 |  |   52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372         
                                                                    44 47
   Legend:   → Mismatch (orange background)
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    → 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: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (REOX_BACHD | Q9KB30)
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: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:0033951    oligosaccharide reducing-end xylanase activity    Catalysis of the hydrolysis of 1,4-beta-D-xylose residues from the reducing end of oligosaccharides.
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
        REOX_BACHD | Q9KB30: 1wu4 1wu5 1wu6 2dro 2drr 2drs 3a3v

(-) Related Entries Specified in the PDB File

1wu4 THE SAME PROTEIN (WILD TYPE).
1wu5 THE SAME PROTEIN (WILD TYPE) COMPLEXED WITH XYLOSE.
1wu6 THE SAME PROTEIN (E70A) COMPLEXED WITH XYLOBIOSE.
2dro THE SAME PROTEIN (D263C)
2drr THE SAME PROTEIN (D263N)
2drs THE SAME PROTEIN (D263S)