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(-) Description

Title :  CRYSTAL STRUCTURE OF XYLANASE (GH10) IN COMPLEX WITH INHIBITOR (XIP)
 
Authors :  F. Payan, P. Leone, C. Furniss, T. Tahir, A. Durand, S. Porciero, P. Manz G. Williamson, H. J. Gilbert, N. Juge, A. Roussel
Date :  19 May 04  (Deposition) - 20 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Alpha Barrel (Xip-I), Beta Alpha Barrel (Xylanase), Hydrolase Inhibitor-Hydrolase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Payan, P. Leone, S. Porciero, C. Furniss, T. Tahir, G. Williamson, A. Durand, P. Manzanares, H. J. Gilbert, N. Juge, A. Roussel
The Dual Nature Of The Wheat Xylanase Protein Inhibitor Xip-I: Structural Basis For The Inhibition Of Family 10 And Family 11 Xylanases.
J. Biol. Chem. V. 279 36029 2004
PubMed-ID: 15181003  |  Reference-DOI: 10.1074/JBC.M404225200

(-) Compounds

Molecule 1 - XYLANASE INHIBITOR PROTEIN I
    Chains: A
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565
    Synonym: XIP-1
 
Molecule 2 - ENDO-1,4-BETA-XYLANASE
    Chains: B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: EMERICELLA NIDULANS
    Expression System Taxid: 162425
    Gene: XLNC
    Organism Scientific: EMERICELLA NIDULANS
    Organism Taxid: 162425
    Synonym: GH10, 34 KDA XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE, X34

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:265 , HOH A:1223 , HOH A:1246 , HOH A:1341 , SER B:210 , ASP B:291 , ASN B:294BINDING SITE FOR RESIDUE NAG A 900
2AC2SOFTWAREASN A:89 , ARG A:135 , HOH A:1354 , HOH B:1254BINDING SITE FOR RESIDUE NAG A 901
3AC3SOFTWARETRP A:201 , GLY A:239 , VAL A:243 , HOH A:1008 , HOH A:1043 , GLN B:87 , HOH B:1032BINDING SITE FOR RESIDUE EDO B 1001
4AC4SOFTWARETYR A:238 , EDO A:1003 , ASP B:49 , GLN B:87BINDING SITE FOR RESIDUE EDO B 1002
5AC5SOFTWARELYS A:246 , ASP B:49 , ALA B:50 , EDO B:1002BINDING SITE FOR RESIDUE EDO A 1003
6AC6SOFTWAREARG A:22 , ASN B:252 , ASN B:256 , HOH B:1224 , HOH B:1264BINDING SITE FOR RESIDUE EDO B 1004
7AC7SOFTWARETHR B:71 , LYS B:75 , LYS B:119 , HOH B:1344BINDING SITE FOR RESIDUE EDO B 1005
8AC8SOFTWAREARG B:158 , PRO B:197 , HOH B:1136 , HOH B:1365BINDING SITE FOR RESIDUE EDO B 1006
9AC9SOFTWARELEU A:269 , TYR A:272 , TRP B:274 , ARG B:275 , ALA B:276 , SER B:277 , HOH B:1218 , HOH B:1374BINDING SITE FOR RESIDUE EDO B 1007

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:66
2A:164 -A:195
3B:254 -B:260

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:36 -Phe A:37
2Tyr A:166 -Pro A:167
3Trp A:256 -Asp A:257
4His B:80 -Thr B:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TA3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH10_2PS51760 Glycosyl hydrolases family 10 (GH10) domain profile.XYNC_EMENI44-325  1B:18-299

(-) Exons   (0, 0)

(no "Exon" information available for 1TA3)

(-) 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:274
 aligned with XIP1_WHEAT | Q8L5C6 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:274
                                    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    
           XIP1_WHEAT    31 AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA 304
               SCOP domains d1ta3a_ A: Xylanase inhibitor protein I, XIP-I                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1ta3A00 A:1-274 Glycosidases                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -----Glyco_hydro_18-1ta3A01 A:6-202                                                                                                                                                                       ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhhhhhh....eeeeeeeee.......ee.....hhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhh.................eeeeee.......hhhhhhhhhhh...........eeeeee......hhhhhhhhh.....eeeee............hhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ta3 A   1 AGGKTGQVTVFWGRNKAEGSLREACDSGMYTMVTMSFLDVFGANGKYHLDLSGHDLSSVGADIKHCQSKGVPVSLSIGGYGTGYSLPSNRSALDLFDHLWNSYFGGSKPSVPRPFGDAWLDGVDLFLEHGTPADRYDVLALELAKHNIRGGPGKPLHLTATVRCGYPPAAHVGRALATGIFERVHVRTYESDKWCNQNLGWEGSWDKWTAAYPATRFYVGLTADDKSHQWVHPKNVYYGVAPVAQKKDNYGGIMLWDRYFDKQTNYSSLIKYYA 274
                                    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    


Chain B from PDB  Type:PROTEIN  Length:301
 aligned with XYNC_EMENI | Q00177 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:301
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326 
           XYNC_EMENI    27 ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNFGWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRYKGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLDSASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEVAITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPKDAYNAIVNALS 327
               SCOP domains d1ta3b_ B: Xylanase A, catalytic core                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1ta3B00 B:1-301 Glycosidases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -Glyco_hydro_10-1ta3B01 B:2-300                                                                                                                                                                                                                                                                             - Pfam domains
         Sec.struct. author .hhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh..hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhh....eeeeeeeee...hhhhhhhhhhhhhh...eeeeee...hhhhh.hhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------GH10_2  PDB: B:18-299 UniProt: 44-325                                                                                                                                                                                                                                                     -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ta3 B   1 ASLNDLFVAAGKSYFGTCSDQALLQNSQNEAIVASQFGVITPENSMKWDALEPSQGNFGWSGADYLVDYATQHNKKVRGHTLVWHSQLPSWVSSIGDANTLRSVMTNHINEVVGRYKGKIMHWDVVNEIFNEDGTFRNSVFYNLLGEDFVRIAFETARAADPDAKLYINDYNLDSASYAKTQAMASYVKKWLAEGVPIDGIGSQAHYSSSHWSSTEAAGALSSLANTGVSEVAITELDIAGAASSDYLNLLNACLNEQKCVGITVWGVSDKDSWRASDSPLLFDGNYQPKDAYNAIVNALS 301
                                    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
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) Gene Ontology  (10, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XIP1_WHEAT | Q8L5C6)
molecular function
    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:0006952    defense response    Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain B   (XYNC_EMENI | Q00177)
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.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XIP1_WHEAT | Q8L5C6: 1om0 1te1

(-) Related Entries Specified in the PDB File

1te1 CRYSTAL STRUCTURE OF FAMILY 11 XYLANASE IN COMPLEX WITH INHIBITOR (XIP-I)