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(-) Description

Title :  CRYSTAL STRUCTURE OF ALKALINE THERMOPHLIC XYLANASE FROM BACILLUS SP. (NCL 86-6-10) WITH COMPLEX XYLOTRIOSE: XYLOTRIOSE CLEAVED TO XYLOBIOSE AND XYLOSE
 
Authors :  L. Satyanarayana, S. M. Gaikwad, H. Balakrishnan, C. G. Suresh
Date :  01 Nov 06  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alkaline Xylanase, Active Site Residues, Three-Dimentional Structure, Xylotrise, Xylobiose, Xylose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Satyanarayana, S. M. Gaikwad, H. Balakrishnan, C. G. Suresh
Crystal Structure Of Alkaline Thermophlic Xylanase From Bacillus Sp. (Ncl 86-6-10) With Complex Xylotriose: Xylotriose Cleaved To Xylobiose And Xylose
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAMILY 11 XYLANASE
    Chains: A, B
    EC Number: 3.2.1.8
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 1409
    Strain: NCL 86-6-10

 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
1BXP2Ligand/IonBETA-D-XYLOBIOPYRANOSE
2XYP2Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BXP1Ligand/IonBETA-D-XYLOBIOPYRANOSE
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BXP1Ligand/IonBETA-D-XYLOBIOPYRANOSE
2XYP1Ligand/IonBETA-D-XYLOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:17 , LEU A:47 , ARG A:49 , TYR A:85 , GLU A:94 , ARG A:129 , PRO A:133 , SER A:134 , GLN A:143BINDING SITE FOR RESIDUE BXP A 1001
2AC2SOFTWAREGLU B:17 , TRP B:19 , LEU B:47 , ARG B:49 , TYR B:85 , GLU B:94 , TYR B:96 , ARG B:129 , PRO B:133 , GLN B:143 , XYP B:3002 , HOH B:3073BINDING SITE FOR RESIDUE BXP B 2001
3AC3SOFTWAREASN A:45 , TYR A:81 , TRP A:104 , ARG A:129 , GLU A:184 , TYR A:186 , HOH A:3062BINDING SITE FOR RESIDUE XYP A 3001
4AC4SOFTWAREASN B:45 , TYR B:81 , TYR B:96 , ARG B:129 , GLN B:143 , TRP B:145 , TYR B:186 , BXP B:2001BINDING SITE FOR RESIDUE XYP B 3002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NQY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:90 -Pro A:91
2Pro A:106 -Pro A:107
3Ser 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 2NQY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NQY)

(-) 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:206
 aligned with Q7SIE3_BACAG | Q7SIE3 from UniProtKB/TrEMBL  Length:207

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         Q7SIE3_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPL 206
               SCOP domains d2nqya_ A: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains 2nqyA00 A:1-206  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeeeeeeeeeeeeeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nqy A   1 EIVTDNSTGNHDGYDYEFWKDSGGSGTMILNSGGTFSASWSSVSNILFRKGKKFNETQTHQQVGNMSISYGANFQPSGNAYLCVYGWTVSPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETDRTNQPSIKGVATFSQYWSTRRSKRTSGTISVSNHFRAWESLGMNMGDMYEVALTVEGYQSSGSANVYSNTLRINGNPL 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      


Chain B from PDB  Type:PROTEIN  Length:206
 aligned with Q7SIE3_BACAG | Q7SIE3 from UniProtKB/TrEMBL  Length:207

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
         Q7SIE3_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPL 206
               SCOP domains d2nqyb_ B: automated matches                                                                                                                                                                                   SCOP domains
               CATH domains 2nqyB00 B:1-206  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
           Pfam domains (1) --------Glyco_hydro_11-2nqyB01 B:9-196                                                                                                                                                              ---------- Pfam domains (1)
           Pfam domains (2) --------Glyco_hydro_11-2nqyB02 B:9-196                                                                                                                                                              ---------- Pfam domains (2)
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeeeeeeeeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeeeeeeeeeeeeeeeeee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nqy B   1 EIVTDNSTGNHDGYDYEFWKDSGGSGTMILNSGGTFSASWSSVSNILFRKGKKFNETQTHQQVGNMSISYGANFQPSGNAYLCVYGWTVSPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETDRTNQPSIKGVATFSQYWSTRRSKRTSGTISVSNHFRAWESLGMNMGDMYEVALTVEGYQSSGSANVYSNTLRINGNPL 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (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 1qh7 2f6b

(-) Related Entries Specified in the PDB File

2f6b THE SAME PROTEIN IN NATIVE FORM