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(-) Description

Title :  CRYSTAL STRUCTURE OF EP COMPLEX 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 :  1.95
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, Ep Complex, 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1AZI2Ligand/IonAZIDE ION
2GOL8Ligand/IonGLYCEROL
3XYS4Ligand/IonXYLOPYRANOSE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2GOL3Ligand/IonGLYCEROL
3XYS2Ligand/IonXYLOPYRANOSE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2GOL5Ligand/IonGLYCEROL
3XYS2Ligand/IonXYLOPYRANOSE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:44 , ASN A:45 , LYS A:48 , TRP A:266 , TRP A:274 , XYS A:452BINDING SITE FOR RESIDUE XYS A 451
02AC2SOFTWARELYS A:48 , HIS A:81 , HIS A:128 , GLN A:205 , GLU A:236 , TRP A:266 , TRP A:274 , XYS A:451 , AZI A:453 , HOH A:1609BINDING SITE FOR RESIDUE XYS A 452
03AC3SOFTWAREHIS A:128 , TYR A:172 , GLN A:205 , HIS A:207 , XYS A:452BINDING SITE FOR RESIDUE AZI A 453
04AC4SOFTWAREGLU B:544 , ASN B:545 , LYS B:548 , GLN B:588 , TRP B:766 , TRP B:774 , XYS B:952 , HOH B:1190 , HOH B:1278BINDING SITE FOR RESIDUE XYS B 951
05AC5SOFTWARELYS B:548 , HIS B:581 , HIS B:628 , GLN B:705 , GLU B:736 , TRP B:766 , TRP B:774 , XYS B:951 , AZI B:953BINDING SITE FOR RESIDUE XYS B 952
06AC6SOFTWAREHIS B:628 , TYR B:672 , GLN B:705 , HIS B:707 , XYS B:952 , GOL B:962BINDING SITE FOR RESIDUE AZI B 953
07AC7SOFTWAREASP 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 1460
08AC8SOFTWAREASP A:408 , ALA A:409 , VAL A:410 , GLY A:411 , GLY A:412 , GLN A:421 , TYR A:423 , ASN A:430 , HOH A:1531BINDING SITE FOR RESIDUE GOL A 1461
09AC9SOFTWARETHR A:4 , GLY A:6 , ALA A:7 , ARG A:36 , GLU A:37 , PHE A:38 , ASN A:39 , LYS A:76 , HOH A:1555 , GLY B:523 , HOH B:1040 , HOH B:1120BINDING SITE FOR RESIDUE GOL A 1462
10BC1SOFTWAREGLN A:77 , ALA A:121 , LYS A:166 , PHE B:561 , SER B:562 , ASP B:565 , HIS B:615 , HOH B:1261BINDING SITE FOR RESIDUE GOL B 960
11BC2SOFTWAREGLN B:577 , GLY B:618 , ILE B:620 , ALA B:621 , ALA B:664 , HOH B:1009 , HOH B:1155BINDING SITE FOR RESIDUE GOL B 961
12BC3SOFTWARETYR B:672 , ASN B:673 , HIS B:707 , ASN B:709 , ARG B:775 , AZI B:953BINDING SITE FOR RESIDUE GOL B 962
13BC4SOFTWAREASP B:825 , VAL B:826 , PRO B:827 , ASN B:828 , ALA B:829 , GLN B:838 , TYR B:840 , HIS B:843 , ASN B:847 , HOH B:1254BINDING SITE FOR RESIDUE GOL B 963
14BC5SOFTWAREASP B:908 , ALA B:909 , VAL B:910 , GLY B:911 , GLY B:912 , GLN B:921 , TYR B:923 , ASN B:930BINDING SITE FOR RESIDUE GOL B 964

(-) 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 2D23)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D23)

(-) Exons   (0, 0)

(no "Exon" information available for 2D23)

(-) 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 d2d23a1 A:1-301 automated matches                                                                                                                                                                                                                                                                            --------------------d2d23a2 A:322-436 automated matches                                                                                 SCOP domains
               CATH domains 2d23A01 A:1-300 Glycosidases                                                                                                                                                                                                                                                                                ------------2d23A02 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.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.............hhhhhh..hhhhhhhhhhhhhh...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
                 2d23 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 d2d23b1 B:501-801 automated matches                                                                                                                                                                                                                                                                          --------------------d2d23b2 B:822-936 automated matches                                                                                 SCOP domains
               CATH domains 2d23B01 B:501-800 Glycosidases                                                                                                                                                                                                                                                                              ------------2d23B02 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.............hhhhhh..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh....eeee..ee........hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhhh..eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh..---------...ee....eeeehhhhh.......eeee...hhhhh.ee.....eee...eeeee........eeeee...hhhh.eee.....eee.....eeee.hhh......eeee....hhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d23 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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  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 2D23)

(-) 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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  2d23
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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 2d22 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
2d22
2d24