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(-) Description

Title :  CATALYSIS AND SPECIFICITY IN ENZYMATIC GLYCOSIDE HYDROLASES: A 2,5B CONFORMATION FOR THE GLYCOSYL-ENZYME INTERMIDIATE REVEALED BY THE STRUCTURE OF THE BACILLUS AGARADHAERENS FAMILY 11 XYLANASE
 
Authors :  E. Sabini, G. Sulzenbacher, M. Dauter, Z. Dauter, P. L. Jorgensen, M. Schulein, C. Dupont, G. J. Davies, K. S. Wilson
Date :  11 May 99  (Deposition) - 17 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyl Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Sabini, G. Sulzenbacher, M. Dauter, Z. Dauter, P. L. Jorgensen, M. Schulein, C. Dupont, G. J. Davies, K. S. Wilson
Catalysis And Specificity In Enzymatic Glycoside Hydrolysis: A 2, 5B Conformation For The Glycosyl-Enzyme Intermediate Revealed By The Structure Of The Bacillus Agaradhaerens Family 11 Xylanase.
Chem. Biol. V. 6 483 1999
PubMed-ID: 10381409  |  Reference-DOI: 10.1016/S1074-5521(99)80066-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Taxid: 1423
    Fragment: FAMILY 11 XYLANASE CATALYTIC DOMAIN
    Organism Scientific: BACILLUS AGARADHAERENS
    Organism Taxid: 76935
    Other Details: B-D-XYLANOPYRANOSIDE PRESENT IN THE ACTIVE SITE

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PCA2Mod. Amino AcidPYROGLUTAMIC ACID
2XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PCA1Mod. Amino AcidPYROGLUTAMIC ACID
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:17 , ARG A:49 , TYR A:85 , GLU A:94 , SER A:134 , HOH A:1088 , HOH A:1220 , HOH A:1279BINDING SITE FOR RESIDUE XYP A 1001
2AC2SOFTWAREGLU B:17 , TRP B:19 , ARG B:49 , TYR B:85 , GLU B:94 , SER B:134 , HOH B:1039 , HOH B:1127 , HOH B:1215 , HOH B:1272 , HOH B:1288BINDING SITE FOR RESIDUE XYP B 1002
3ACAAUTHORGLU A:184CATALYTIC ACID / BASE
4ACBAUTHORGLU B:184CATALYTIC ACID / BASE
5NUAAUTHORGLU A:94CATALYTIC NUCLEOPHILE
6NUBAUTHORGLU B:94CATALYTIC NUCLEOPHILE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QH7)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:90 -Pro A:91
2Pro A:106 -Pro A:107
3Asp B:90 -Pro B:91
4Pro B:106 -Pro B:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QH7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QH7)

(-) Exons   (0, 0)

(no "Exon" information available for 1QH7)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:207
 aligned with Q7SIE3_BACAG | Q7SIE3 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q7SIE3_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
               SCOP domains d1qh7a_ A: Xylanase II                                                                                                                                                                                          SCOP domains
               CATH domains -1qh7A00 A:2-207  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee......hhhh..eeeeeeeeeeee.eeeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeee...........eeeeeeee.....eeeeehhhhhhhhhhh.....eeeeeeeeeeee..eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qh7 A   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
                            |                                                                                                                                                                                                              
                            1-PCA                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q7SIE3_BACAG | Q7SIE3 from UniProtKB/TrEMBL  Length:207

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q7SIE3_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
               SCOP domains d1qh7b_ B: Xylanase II                                                                                                                                                                                          SCOP domains
               CATH domains -1qh7B00 B:2-207  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
           Pfam domains (1) --------Glyco_hydro_11-1qh7B01 B:9-196                                                                                                                                                              ----------- Pfam domains (1)
           Pfam domains (2) --------Glyco_hydro_11-1qh7B02 B:9-196                                                                                                                                                              ----------- Pfam domains (2)
         Sec.struct. author ......eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee......hhhh..eeeeeeeeeeee..eeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeee..eee..eee.eeeeeeee.....eeee.hhhhhhhhhh......eeeeeeeeeeee..eeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qh7 B   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
                            1-PCA
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7SIE3_BACAG | Q7SIE3)
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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        Q7SIE3_BACAG | Q7SIE3: 1h4g 1qh6 2f6b 2nqy

(-) Related Entries Specified in the PDB File

1qh6