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(-) Description

Title :  CRYSTAL STRUCTURE OF FAMILY 11 XYLANASE IN COMPLEX WITH INHIBITOR (XIP-I)
 
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 :  24 May 04  (Deposition) - 20 Jul 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta/Alpha Barrel (Xip-I) And Beta Jelly Roll (Gh11), 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-XYLANASE
    Chains: B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: PENICILLIUM FUNICULOSUM
    Expression System Taxid: 28572
    Gene: XYNC
    Organism Scientific: PENICILLIUM FUNICULOSUM
    Organism Taxid: 28572
    Synonym: GH11

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:165 , TYR A:166 , PRO A:167 , LYS A:262 , GLN A:263 , ASN A:265BINDING SITE FOR RESIDUE NAG A 900
02AC2SOFTWAREASN A:89 , HOH A:964 , HOH A:1009BINDING SITE FOR RESIDUE NAG A 901
03AC3SOFTWARETHR A:222 , ASP A:224 , SER A:227 , TRP A:256 , HOH A:961BINDING SITE FOR RESIDUE EDO A 902
04AC4SOFTWAREALA A:214 , ARG A:216BINDING SITE FOR RESIDUE EDO A 903
05AC5SOFTWAREARG A:22 , HOH A:943BINDING SITE FOR RESIDUE EDO A 904
06AC6SOFTWARELEU A:199 , GLY A:200 , GLY A:203BINDING SITE FOR RESIDUE EDO A 905
07AC7SOFTWAREALA A:177 , HOH A:1047BINDING SITE FOR RESIDUE EDO A 906
08AC8SOFTWARESER A:68 , GLY A:70 , ASP B:41 , CYS B:42 , GLU B:179BINDING SITE FOR RESIDUE EDO B 207
09AC9SOFTWAREPHE B:65 , SER B:91 , TYR B:92 , EDO B:211BINDING SITE FOR RESIDUE EDO B 208
10BC1SOFTWARECYS A:25 , GLY A:28 , LYS A:69BINDING SITE FOR RESIDUE EDO A 907
11BC2SOFTWARELEU B:104 , GLY B:105 , ILE B:116 , LEU B:161BINDING SITE FOR RESIDUE EDO B 210
12BC3SOFTWAREASN A:15 , LYS A:16 , SER A:52 , LYS B:143 , EDO B:208BINDING SITE FOR RESIDUE EDO B 211
13BC4SOFTWAREGLN A:67 , GLY A:70 , PRO A:72 , HOH A:919 , ASN B:20 , GLY B:22BINDING SITE FOR RESIDUE EDO A 908

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:36 -Phe A:37
2Tyr A:166 -Pro A:167
3Trp A:256 -Asp A:257
4Asp B:81 -Pro B:82
5Gly B:105 -Gln B:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TE1)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_3PS51761 Glycosyl hydrolases family 11 (GH11) domain profile.XYNC_TALFU35-223  1B:1-189
2GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNC_TALFU116-126  1B:82-92

(-) Exons   (0, 0)

(no "Exon" information available for 1TE1)

(-) 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 d1te1a_ A: Xylanase inhibitor protein I, XIP-I                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1te1A00 A:1-274 Glycosidases                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -----Glyco_hydro_18-1te1A01 A:6-202                                                                                                                                                                       ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhhhhhh....eeeeeee................hhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhhhhhhhh.................eeeeee.......hhhhhhhhhhh...........eeeeeee.....hhhhhhhhh.....eeeee............hhhhhhhhhhhhh...eeeeeee.........hhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1te1 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:190
 aligned with XYNC_TALFU | Q9HFH0 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:190
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
           XYNC_TALFU    34 QSITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYSGEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVNQPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSSTITVS 223
               SCOP domains d1te1b_ B: Xylanase II                                                                                                                                                                         SCOP domains
               CATH domains 1te1B00 B:0-189  [code=2.60.120.180, no name defined]                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee....eeeeee....eeeeee....eeeeeee...eeeeeeee......eeeeeeeeeee..eeeeeeeeee...eeeeeeeee.......................eeeeeeeee......eeeeeeee.......eeeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -GH11_3  PDB: B:1-189 UniProt: 35-223                                                                                                                                                          PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------GH11_1     ------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1te1 B   0 QSITTSQTGTNNGYYYSFWTNGGGEVTYTNGDNGEYSVTWVDCGDFTSGKGWNPANAQTVTYSGEFNPSGNAYLAVYGWTTDPLVEYYILESYGTYNPSSGLTSLGQVTSDGGTYDIYSTQRVNQPSIEGTSTFNQYWSVRTEKRVGGTVTTANHFAAWKALGLEMGTYNYMIVSTEGYESSGSSTITVS 189
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189
   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: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

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_TALFU | Q9HFH0)
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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  XYNC_TALFU | Q9HFH0
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 Related Entries

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

UniProtKB/Swiss-Prot
        XIP1_WHEAT | Q8L5C6: 1om0 1ta3
        XYNC_TALFU | Q9HFH0: 3wp3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TE1)