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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86 COMPLEXED WITH GALACTOSE
 
Authors :  Z. Fujimoto, A. Kuno, S. Kaneko, H. Kobayashi, I. Kusakabe, H. Mizuno
Date :  27 Dec 01  (Deposition) - 20 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Barrel, Protein-Sugar Complex, Carbohydrate Binding Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Fujimoto, A. Kuno, S. Kaneko, H. Kobayashi, I. Kusakabe, H. Mizuno
Crystal Structures Of The Sugar Complexes Of Streptomyces Olivaceoviridis E-86 Xylanase: Sugar Binding Structure Of The Family 13 Carbohydrate Binding Module.
J. Mol. Biol. V. 316 65 2002
PubMed-ID: 11829503  |  Reference-DOI: 10.1006/JMBI.2001.5338
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-D-XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: STREPTOMYCES OLIVACEOVIRIDIS
    Organism Taxid: 1921
    Strain: E-86

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GAL4Ligand/IonBETA-D-GALACTOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:325 , VAL A:326 , PRO A:327 , ASN A:328 , GLN A:338 , TYR A:340 , HIS A:343 , ASN A:347 , HOH A:602 , HOH A:625BINDING SITE FOR RESIDUE GAL A 461
2AC2SOFTWAREASP A:408 , ALA A:409 , GLY A:411 , GLN A:421 , TYR A:423 , ASN A:430BINDING SITE FOR RESIDUE GAL A 471
3AC3SOFTWAREASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , GLN B:838 , TYR B:840 , HIS B:843 , ASN B:847BINDING SITE FOR RESIDUE GAL B 961
4AC4SOFTWAREASP B:908 , ALA B:909 , VAL B:910 , GLY B:911 , GLY B:912 , GLN B:921 , ASN B:930BINDING SITE FOR RESIDUE GAL B 971

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:168 -A:201
2A:254 -A:260
3A:323 -A:342
4A:365 -A:382
5A:406 -A:425
6B:668 -B:701
7B:754 -B:760
8B:823 -B:842
9B:865 -B:882
10B:906 -B:925

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:81 -Thr A:82
2His B:581 -Thr B:582

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ISZ)

(-) 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:427
 aligned with Q7SI98_STROI | Q7SI98 from UniProtKB/TrEMBL  Length:436

    Alignment length:436
                                    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       410       420       430      
         Q7SI98_STROI     1 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT 436
               SCOP domains d1isza2 A:1-303 Xylanase A, catalytic core                                                                                                                                                                                                                                                                     ---------d1isza1 A:313-436 Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain)                                     SCOP domains
               CATH domains 1iszA02 A:1-300 Glycosidases                                                                                                                                                                                                                                                                                ------------1iszA01 A:313-434  [code=2.80.10.50, no name defined]                                                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee...............hhhhh.hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeee..ee........hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh..---------..eee.....eeehhhhh.......eee....hhhhh.ee.....eee...eeeee........eeeee...hhhh.eee.....eee.....eeee.hhh......eeee....hhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1isz A   1 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGG---------GQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT 436
                                    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  |      -  |    320       330       340       350       360       370       380       390       400       410       420       430      
                                                                                                                                                                                                                                                                                                                                        303       313                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with Q7SI98_STROI | Q7SI98 from UniProtKB/TrEMBL  Length:436

    Alignment length:436
                                    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       410       420       430      
         Q7SI98_STROI     1 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGGSSTPPPSGGGQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT 436
               SCOP domains d1iszb2 B:501-803 Xylanase A, catalytic core                                                                                                                                                                                                                                                                   ---------d1iszb1 B:813-936 Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain)                                     SCOP domains
               CATH domains 1iszB02 B:501-800 Glycosidases                                                                                                                                                                                                                                                                              ------------1iszB01 B:813-934  [code=2.80.10.50, no name defined]                                                                     -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee...............hhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeee..ee........hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh..---------..eee.....eeehhhhh.......eee....hhhhh.ee.....eee...eeeee......eeeeeee...hhhh.eee.....eee.....eeee.hhh......eeee....hhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1isz B 501 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVNEAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGG---------GQIKGVGSGRCLDVPNASTTDGTQVQLYDCHSATNQQWTYTDAGELRVYGDKCLDAAGTGNGTKVQIYSCWGGDNQKWRLNSDGSIVGVQSGLCLDAVGGGTANGTLIQLYSCSNGSNQRWTRT 936
                                   510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800  |      -  |    820       830       840       850       860       870       880       890       900       910       920       930      
                                                                                                                                                                                                                                                                                                                                        803       813
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ISZ)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7SI98_STROI | Q7SI98)
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.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7SI98_STROI | Q7SI98: 1isv 1isw 1isx 1isy 1it0 1v6u 1v6v 1v6w 1v6x 1v6y 1xyf 2d1z 2d20 2d22 2d23 2d24 2g3i 2g3j 2g4f

(-) Related Entries Specified in the PDB File

1isv 1ISV CONTAINS THE SAME PROTEIN COMPLEXED WITH XYLOSE.
1isw 1ISW CONTAINS THE SAME PROTEIN COMPLEXED WITH XYLOBIOSE.
1isx 1ISX CONTAINS THE SAME PROTEIN COMPLEXED WITH XYLOTRIOSE.
1isy 1ISY CONTAINS THE SAME PROTEIN COMPLEXED WITH GLUCOSE.
1it0 1IT0 CONTAINS THE SAME PROTEIN COMPLEXED WITH LACTOSE.
1xyf 1XYF CONTAINS THE SAME PROTEIN(NON-COMPLEXED STRUCTURE).