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(-) Description

Title :  STRUCTURE OF A COLD-ADAPTED FAMILY 8 XYLANASE
 
Authors :  D. De Vos, T. Collins, A. Hoyoux, S. N. Savvides, C. Gerday, J. J. Van Beeumen, G. Feller
Date :  02 Nov 04  (Deposition) - 11 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Xylan Degradation, Psychrophilic, Cold Adaptation, Temperature, Glycosyl Hydrolase, Family 8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Collins, D. De Vos, A. Hoyoux, S. N. Savvides, C. Gerday, J. Van Beeumen, G. Feller
Study Of The Active Site Residues Of A Glycoside Hydrolase Family 8 Xylanase
J. Mol. Biol. V. 354 425 2005
PubMed-ID: 16246370  |  Reference-DOI: 10.1016/J.JMB.2005.09.064
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE
    Chains: A
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOALTEROMONAS HALOPLANKTIS
    Organism Taxid: 228

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1XYP3Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:280 , GLN A:327 , TYR A:378 , ASN A:382 , XYP A:501 , HOH A:866BINDING SITE FOR RESIDUE XYP A 500
2AC2SOFTWAREPHE A:280 , XYP A:500 , XYP A:502 , HOH A:920BINDING SITE FOR RESIDUE XYP A 501
3AC3SOFTWAREARG A:76 , GLN A:78 , PHE A:280 , ASP A:281 , ARG A:284 , TYR A:380 , XYP A:501 , HOH A:914 , HOH A:916 , HOH A:923BINDING SITE FOR RESIDUE XYP A 502

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:324 -A:339

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:246 -Pro A:247

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XWQ)

(-) Exons   (0, 0)

(no "Exon" information available for 1XWQ)

(-) 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:404
 aligned with Q8RJN8_PSEHA | Q8RJN8 from UniProtKB/TrEMBL  Length:426

    Alignment length:404
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421    
         Q8RJN8_PSEHA    22 AFNNNPSSVGAYSSGTYRNLAQEMGKTNIQQKVNSTFDNMFGYNNTQQLYYPYTENGVYKAHYIKAINPDEGDDIRTEGQSWGMTAAVMLNKQEEFDNLWRFAKAYQKNPDNHPDAKKQGVYAWKLKLNQNGFVYKVDEGPAPDGEEYFAFALLNASARWGNSGEFNYYNDAITMLNTIKNKLMENQIIRFSPYIDNLTDPSYHIPAFYDYFANNVTNQADKNYWRQVATKSRTLLKNHFTKVSGSPHWNLPTFLSRLDGSPVIGYIFNGQANPGQWYEFDAWRVIMNVGLDAHLMGAQAWHKSAVNKALGFLSYAKTNNSKNCYEQVYSYGGAQNRGCAGEGQKAANAVALLASTNAGQANEFFNEFWSLSQPTGDYRYYNGSLYMLAMLHVSGNFKFYNNTF 425
               SCOP domains d1xwqa_ A: Endo-1,4-beta-xylanase                                                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1xwqA00 A:1-404  [code=1.50.10.10, no name defined]                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------Glyco_hydro_8-1xwqA01 A:27-395                                                                                                                                                                                                                                                                                                                                                   --------- Pfam domains
         Sec.struct. author .........hhhhhh...hhhhhh...hhhhhhhhhhhhhh........eeeeee..eeeeeeeee.......eeehhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhh...eeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhee..ee..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh................................ee....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.........ee..ee......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xwq A   1 AFNNNPSSVGAYSSGTYRNLAQEMGKTNIQQKVNSTFDNMFGYNNTQQLYYPYTENGVYKAHYIKAINPDEGDDIRTQGQSWGMTAAVMLNKQEEFDNLWRFAKAYQKNPDNHPDAKKQGVYAWKLKLNQNGFVYKVDEGPAPDGEEYFAFALLNASARWGNSGEFNYYNDAITMLNTIKNKLMENQIIRFSPYIDNLTDPSYHIPAFYDYFANNVTNQADKNYWRQVATKSRTLLKNHFTKVSGSPHWNLPTFLSRLDGSPVIGYIFNGQANPGQWYEFDAWRVIMNVGLDAHLMGAQAWHKSAVNKALGFLSYAKTNNSKNCYEQVYSYGGAQNRGCAGEGQKAANAVALLASTNAGQANEFFNEFWSLSQPTGDYRYYNGSLYMLAMLHVSGNFKFYNNTF 404
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400
   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: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: 6_Hairpin (120)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q8RJN8_PSEHA | Q8RJN8)
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: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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  1xwq
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 Related Entries

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

UniProtKB/TrEMBL
        Q8RJN8_PSEHA | Q8RJN8: 1h12 1h13 1h14 1xw2 1xwt 2a8z 2b4f

(-) Related Entries Specified in the PDB File

1h12
1h13
1h14
1xwt THE SAME PROTEIN AT 1.3 A