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(-) Description

Title :  CRYSTAL STRUCTURE OF COVALENT GLYCOSYL-ENZYME INTERMEDIATE OF CATALYTIC-SITE MUTANT XYLANASE FROM STREPTOMYCES OLIVACEOVIRIDIS E-86
 
Authors :  R. Suzuki, A. Kuno, Z. Fujimoto, S. Ito, S. I. Kawahara, S. Kaneko, T. Has K. Taira
Date :  02 Sep 05  (Deposition) - 10 Oct 06  (Release) - 15 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tim-Barrel, Retaining Enzyme, Catalytic-Site Mutant, Chemical Rescue, Covalent Glycosyl-Enzyme Intermediate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Suzuki, Z. Fujimoto, S. Ito, S. Kawahara, S. Kaneko, K. Taira, T. Hasegawa, A. Kuno
Crystallographic Snapshots Of An Entire Reaction Cycle For Retaining Xylanase From Streptomyces Olivaceoviridis E-86
J. Biochem. V. 146 61 2009
PubMed-ID: 19279191  |  Reference-DOI: 10.1093/JB/MVP047
(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 Plasmid: PQE60
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: STREPTOMYCES OLIVACEOVIRIDIS
    Organism Taxid: 1921
    Strain: E-86
    Synonym: GLYCOSIDE HYDROLASE FAMILY 10 XYLANASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 17)

Asymmetric Unit (3, 17)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
3XYS4Ligand/IonXYLOPYRANOSE
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
3XYS2Ligand/IonXYLOPYRANOSE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
3XYS2Ligand/IonXYLOPYRANOSE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:48 , HIS A:81 , HIS A:128 , GLN A:205 , GLU A:236 , TRP A:266 , XYS A:451 , HOH A:1000BINDING SITE FOR RESIDUE XYS A 452
02AC2SOFTWAREGLU A:44 , ASN A:45 , LYS A:48 , GLN A:88 , TRP A:266 , TRP A:274 , XYS A:452 , HOH A:1010 , HOH A:1175 , HOH A:1209 , HOH A:1230BINDING SITE FOR RESIDUE XYS A 451
03AC3SOFTWARELYS B:548 , HIS B:581 , HIS B:628 , GLN B:705 , GLU B:736 , TRP B:766 , TRP B:774 , XYS B:951 , HOH B:985 , HOH B:1225BINDING SITE FOR RESIDUE XYS B 952
04AC4SOFTWAREGLU B:544 , ASN B:545 , LYS B:548 , GLN B:588 , TRP B:766 , TRP B:774 , XYS B:952 , HOH B:1058 , HOH B:1080 , HOH B:1122 , HOH B:1179BINDING SITE FOR RESIDUE XYS B 951
05AC5SOFTWAREHOH A:1020 , SER B:631 , ASP B:633 , ARG B:639 , ASP B:640 , HOH B:1165 , HOH B:1394BINDING SITE FOR RESIDUE SO4 A 968
06AC6SOFTWARESER A:62 , GLY A:413 , THR A:414 , ALA A:415 , HOH A:1060 , HOH A:1080BINDING SITE FOR RESIDUE SO4 A 969
07AC7SOFTWAREHIS B:707 , ARG B:775 , HOH B:1245BINDING SITE FOR RESIDUE SO4 B 970
08AC8SOFTWAREHIS A:207 , ASN A:209 , ARG A:275BINDING SITE FOR RESIDUE SO4 A 971
09AC9SOFTWAREHIS A:343 , SER A:344BINDING SITE FOR RESIDUE SO4 A 972
10BC1SOFTWAREASP A:408 , ALA A:409 , GLY A:411 , GLY A:412 , GLN A:421 , ASN A:430 , HOH A:1018BINDING SITE FOR RESIDUE GOL A 960
11BC2SOFTWAREALA A:368 , ASN A:387 , GLN A:402 , SER B:710 , GLY B:711 , GLN B:740 , HOH B:1405BINDING SITE FOR RESIDUE GOL B 961
12BC3SOFTWAREASP A:325 , VAL A:326 , PRO A:327 , ASN A:328 , GLN A:338 , TYR A:340 , HIS A:343 , ASN A:347BINDING SITE FOR RESIDUE GOL A 962
13BC4SOFTWAREASP A:65 , ASN A:69 , HIS A:115 , TYR A:116 , LYS A:119BINDING SITE FOR RESIDUE GOL A 963
14BC5SOFTWARELYS B:524 , THR B:771 , ASP B:772 , SER B:773 , HOH B:1004 , HOH B:1124BINDING SITE FOR RESIDUE GOL B 964
15BC6SOFTWAREASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , GLN B:838 , HIS B:843 , ASN B:847 , HOH B:1418BINDING SITE FOR RESIDUE GOL B 965
16BC7SOFTWAREARG B:659 , PRO B:698BINDING SITE FOR RESIDUE GOL B 966
17BC8SOFTWARETHR A:31 , SER A:35 , TRP A:70 , HOH A:1062 , HOH A:1078 , SER B:528 , HOH B:1296BINDING SITE FOR RESIDUE GOL B 967

(-) SS Bonds  (10, 10)

Asymmetric 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  (3, 3)

Asymmetric Unit
No.Residues
1His A:81 -Thr A:82
2His B:581 -Thr B:582
3Arg B:935 -Thr B:936

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D22)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D22)

(-) Exons   (0, 0)

(no "Exon" information available for 2D22)

(-) Sequences/Alignments

Asymmetric 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 d2d22a1 A:1-301 automated matches                                                                                                                                                                                                                                                                            --------------------d2d22a2 A:322-436 automated matches                                                                                 SCOP domains
               CATH domains 2d22A01 A:1-300 Glycosidases                                                                                                                                                                                                                                                                                ------------2d22A02 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...............hhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh....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
                 2d22 A   1 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVSHAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGG---------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 d2d22b1 B:501-801 automated matches                                                                                                                                                                                                                                                                          --------------------d2d22b2 B:822-936 automated matches                                                                                 SCOP domains
               CATH domains 2d22B01 B:501-800 Glycosidases                                                                                                                                                                                                                                                                              ------------2d22B02 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.......hhhhhhhhhhhhhhhhhh....eeee..ee........hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh..---------...ee.....eeehhhhh.......eee..........ee.....eee...eeeee........eeeee...hhhh.eee.....eee.....eeee.hhh......eeee....hhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d22 B 501 AESTLGAAAAQSGRYFGTAIASGKLGDSAYTTIASREFNMVTAENEMKIDATEPQRGQFNFSAGDRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSTLRQAMIDHINGVMGHYKGKIAQWDVVSHAFSDDGSGGRRDSNLQRTGNDWIEVAFRTARAADPAAKLCYNDYNIENWTWAKTQGVYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGASSSTYAAVTNDCLAVSRCLGITVWGVRDTDSWRSGDTPLLFNGDGSKKAAYTAVLNALNGG---------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)
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  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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D22)

(-) Gene Ontology  (7, 7)

Asymmetric 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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  2d22
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1isw THE WILD-TYPE ENZYME IN COMPLEX WITH XYLOBIOSE.
1isx THE WILD-TYPE ENZYME IN COMPLEX WITH XYLOTRIOSE.
1xyf THE WILD-TYPE ENZYME OF SEA.
2d1z FREE-MODE OF THE SAME PROTEIN.
2d20
2d23
2d24