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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRITICUM AESTIVUM XYLANASE INHIBITOR-IIA IN COMPLEX WITH BACILLUS SUBTILIS XYLANASE
 
Authors :  S. Sansen, A. Pollet, G. Raedschelders, K. Gebruers, A. Rabijns, C. M. C
Date :  07 May 09  (Deposition) - 30 Jun 09  (Release) - 30 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Two Beta-Barrel Domain, Beta-Jelly Roll, Hydrolase Inhibitor- Hydrolase Complex, Protein-Protein Complex, Xylan Degradation, Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Pollet, S. Sansen, G. Raedschelders, K. Gebruers, A. Rabijns, J. A. Delcour, C. M. Courtin
Identification Of Structural Determinants For Inhibition Strength And Specificity Of Wheat Xylanase Inhibitors Taxi-Ia And Taxi-Iia
Febs J. V. 276 3916 2009
PubMed-ID: 19769747  |  Reference-DOI: 10.1111/J.1742-4658.2009.07105.X

(-) Compounds

Molecule 1 - XYLANASE INHIBITOR
    ChainsA, C
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZAC
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneXYNA
    Organism CommonWHEAT
    Organism ScientificTRITICUM AESTIVUM
    Organism Taxid4565
    SynonymXYLANASE INHIBITOR IIA
 
Molecule 2 - ENDO-1,4-BETA-XYLANASE A
    ChainsB, D
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneXYNA
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423
    SynonymXYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3HD8)

(-) Sites  (0, 0)

(no "Site" information available for 3HD8)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:41 -A:126
2A:57 -A:82
3A:68 -A:94
4A:169 -A:380
5A:284 -A:329
6C:41 -C:126
7C:57 -C:82
8C:68 -C:94
9C:169 -C:380
10C:284 -C:329

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:279 -Pro A:280
2Ser B:74 -Pro B:75
3Ala C:279 -Pro C:280
4Ser D:74 -Pro D:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HD8)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACSU103-113
 
  2B:75-85
D:75-85
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACSU197-208
 
  2B:169-180
D:169-180
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACSU103-113
 
  1B:75-85
-
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACSU197-208
 
  1B:169-180
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH11_1PS00776 Glycosyl hydrolases family 11 (GH11) active site signature 1.XYNA_BACSU103-113
 
  1-
D:75-85
2GH11_2PS00777 Glycosyl hydrolases family 11 (GH11) active site signature 2.XYNA_BACSU197-208
 
  1-
D:169-180

(-) Exons   (0, 0)

(no "Exon" information available for 3HD8)

(-) 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:370
 aligned with Q53IQ4_WHEAT | Q53IQ4 from UniProtKB/TrEMBL  Length:389

    Alignment length:386
                                    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      
         Q53IQ4_WHEAT     1 KGLPVLAPVTKDTATSLYTIPFHDGASLVLDVAGLLVWSTCEGGQSPAEIACSSPTCLLANAYPAPGCPAPSCGSDRHDKPCTAYPSNPVTGACAAGSLFHTRFAANTTDGNKPVSEVNVRVLAACAPSKLLASLPRGSTGVAGLAGSGLALPSQVASAQKVANKFLLCLPTGGPGVAIFGGGPLPWPQFTQSMDYTPLVAKGGSPAHYISARSIKVENTRVPISERALATGGVMLSTRLPYVLLRRDVYRPLVDAFTKALAAQPANGAPVARAVKPVAPFELCYDTKTLGNNPGGYWVPNVLLELDGGSDWALTGKNSMVDVKPGTACVAFVEMKGVDAGDGSAPAVILGGAQMEDFVLDFDMEKKRLGFLRLPHFTGCSSFNFA 386
               SCOP domains d3hd8a_ A: Xylanase inhibitor TAXI-I                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 3hd8A01 A:1-182 Acid Proteases                                                                                                                                                        3hd8A02 A:183-386 Acid Proteases                                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......eeeeee..eeeeee.....eee....----......hhhhhhhh.........---------...ee............eeeeeeeeeeeee....eeeeeeeeeeeee.hhhhhh.....eeeeee......hhhhhhhhhhh...eeeee......eeeee......hhhhhh..eeee..........ee.eeeeee..ee............eee......eeehhhhhhhhhhhhhhhhhh.---......ee........eee.hhh.ee..ee....eeeee....eeeehhhhheeeee..eeee.eee.............eeehhhhh..eeeeee....eeeeee.....hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd8 A   1 EGLPVLAPVTKDTATSLYTIPFHDGASLVLDVAGLLVWSTCEG----AEIACSSPTCLLANAYPAPGCPA---------KPCTAYPSNPVTGACAAGSLFHTRFAANTTDGNKPVSEVNVRVLAACAPSKLLASLPRGSTGVAGLAGSGLALPSQVASAQKVPNKFLLCLPTGGPGVAIFGGGPLPWPQFTQSMDYTPLVAKGGSPAHYISARSIKVENTRVPISERALATGGVMLSTRLPYVLLRRDVYRPLVDAFTKALAAQ---GAPVARAVKPVAPFELCYDTKTLGNNPGGYWVPNVLLELDGGSDWAMTGKNSMVDVKPGTACVAFVEMKGVDAGDGSAPAVILGGAQMEDFVLDFDMEKKRLGFLRLPHFTGCSSFNFA 386
                                    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      
                                                                     43   48                    70        80                                                                                                                                                                                     264 268                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:184
 aligned with XYNA_BACSU | P18429 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:184
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
           XYNA_BACSU    30 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d3hd8b_ B: Xylanase II                                                                                                                                                                   SCOP domains
               CATH domains 3hd8B00 B:2-185  [code=2.60.120.180, no name defined]                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee.........eeeehhhhhhhhhh.......eeeeeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd8 B   2 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    

Chain C from PDB  Type:PROTEIN  Length:368
 aligned with Q53IQ4_WHEAT | Q53IQ4 from UniProtKB/TrEMBL  Length:389

    Alignment length:385
                                    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     
         Q53IQ4_WHEAT     1 KGLPVLAPVTKDTATSLYTIPFHDGASLVLDVAGLLVWSTCEGGQSPAEIACSSPTCLLANAYPAPGCPAPSCGSDRHDKPCTAYPSNPVTGACAAGSLFHTRFAANTTDGNKPVSEVNVRVLAACAPSKLLASLPRGSTGVAGLAGSGLALPSQVASAQKVANKFLLCLPTGGPGVAIFGGGPLPWPQFTQSMDYTPLVAKGGSPAHYISARSIKVENTRVPISERALATGGVMLSTRLPYVLLRRDVYRPLVDAFTKALAAQPANGAPVARAVKPVAPFELCYDTKTLGNNPGGYWVPNVLLELDGGSDWALTGKNSMVDVKPGTACVAFVEMKGVDAGDGSAPAVILGGAQMEDFVLDFDMEKKRLGFLRLPHFTGCSSFNF 385
               SCOP domains d3hd8c_ C: Xylanase inhibitor TAXI-I                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3hd8C01 C:1-182 Acid Proteases                                                                                                                                                        3hd8C02 C:183-385 Acid Proteases                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee......eeeeee..eeeeee.....eee....-----.....hhhhhhhh.........---------...ee............eeeeeeeeeeeee....eeeeeeeeeeeee.hhhhhh.....eeeeee......hhhhhhhhhhh...eeeee.....eeeeee......hhhhhh..eeee..........ee.eeeeee..ee............eee......eeehhhhhhhhhhhhhhhhhh.---......ee........eee.hhh.ee..ee....eeeee...eeeeehhhhheeeee..eeee.eee.............eeehhhhhh.eeeeee....eeeeee.....hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd8 C   1 EGLPVLAPVTKDTATSLYTIPFHDGASLVLDVAGLLVWSTCEG-----EIACSSPTCLLANAYPAPGCPA---------KPCTAYPSNPVTGACAAGSLFHTRFAANTTDGNKPVSEVNVRVLAACAPSKLLASLPRGSTGVAGLAGSGLALPSQVASAQKVPNKFLLCLPTGGPGVAIFGGGPLPWPQFTQSMDYTPLVAKGGSPAHYISARSIKVENTRVPISERALATGGVMLSTRLPYVLLRRDVYRPLVDAFTKALAAQ---GAPVARAVKPVAPFELCYDTKTLGNNPGGYWVPNVLLELDGGSDWAMTGKNSMVDVKPGTACVAFVEMKGVDAGDGSAPAVILGGAQMEDFVLDFDMEKKRLGFLRLPHFTGCSSFNF 385
                                    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     
                                                                     43    49                   70        80                                                                                                                                                                                     264 268                                                                                                                     

Chain D from PDB  Type:PROTEIN  Length:184
 aligned with XYNA_BACSU | P18429 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:184
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
           XYNA_BACSU    30 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFSNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d3hd8d_ D: Xylanase II                                                                                                                                                                   SCOP domains
               CATH domains 3hd8D00 D:2-185  [code=2.60.120.180, no name defined]                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee........eeeeehhhhhhhhhh.......eeeeeeeeeeeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hd8 D   2 STDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    

   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 Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HD8)

(-) Gene Ontology  (10, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (Q53IQ4_WHEAT | Q53IQ4)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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.
biological process
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    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.

Chain B,D   (XYNA_BACSU | P18429)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XYNA_BACSU | P184291axk 1xxn 2b42 2b45 2b46 2dcy 2dcz 2qz3 2z79 3exu 5k9y

(-) Related Entries Specified in the PDB File

1t6e CRYSTAL STRUCTURE OF THE TRITICUM AESTIVUM XYLANASE INHIBITOR I
1t6g CRYSTAL STRUCTURE OF THE TRITICUM AESTIVUM XYLANASE INHIBITOR-I IN COMPLEX WITH ASPERGILLUS NIGER XYLANASE-I
2b42 CRYSTAL STRUCTURE OF THE TRITICUM XYLANSE INHIBITOR-I IN COMPLEX WITH BACILLUS SUBTILIS XYLANASE