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(-) Description

Title :  STREPTOMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13
 
Authors :  V. Notenboom, A. B. Boraston, S. J. Williams, D. G. Kilburn, D. R. Rose
Date :  19 Dec 01  (Deposition) - 19 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Carbohydrate Binding Module, Cbm13 Xylan Binding Domain, Lectin-Like Ricin B-Like, Beta-Trefoil Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Notenboom, A. B. Boraston, S. J. Williams, D. G. Kilburn, D. R. Rose
High-Resolution Crystal Structures Of The Lectin-Like Xylan Binding Domain From Streptomyces Lividans Xylanase 10A With Bound Substrates Reveal A Novel Mode Of Xylan Binding.
Biochemistry V. 41 4246 2002
PubMed-ID: 11914070  |  Reference-DOI: 10.1021/BI015865J

(-) Compounds

Molecule 1 - ENDO-1,4-BETA-XYLANASE A
    ChainsA
    EC Number3.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCARBOHYDRATE BINDING MODULE (RESIDUES 348-477)
    Organism ScientificSTREPTOMYCES LIVIDANS
    Organism Taxid1916
    SynonymXYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:60 , ALA A:61 , GLN A:71 , TRP A:76 , ASN A:80 , SER A:87 , HOH A:175 , HOH A:209 , HOH A:311BINDING SITE FOR RESIDUE GOL A 530
2AC2SOFTWAREASP A:18 , VAL A:19 , PRO A:20 , ASP A:21 , GLN A:31 , HIS A:36 , ASN A:40 , HOH A:344 , HOH A:359BINDING SITE FOR RESIDUE GOL A 531

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:16 -A:35
2A:58 -A:75
3A:99 -A:118

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KNL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.XYNA_STRLI361-477  1A:13-129

(-) Exons   (0, 0)

(no "Exon" information available for 1KNL)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:126
 aligned with XYNA_STRLI | P26514 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:126
                                   361       371       381       391       401       411       421       431       441       451       461       471      
           XYNA_STRLI   352 DGGQIKGVGSGRCLDVPDASTSDGTQLQLWDCHSGTNQQWAATDAGELRVYGDKCLDAAGTSNGSKVQIYSCWGGDNQKWRLNSDGSVVGVQSGLCLDAVGNGTANGTLIQLYTCSNGSNQRWTRT 477
               SCOP domains d1knla_ A: Xylan binding domain, CBM13 (Endo-1,4-beta-xylanase C-terminal domain)                                              SCOP domains
               CATH domains 1knlA00 A:4-129  [code=2.80.10.50, no name defined]                                                                            CATH domains
               Pfam domains Ricin_B_lectin-1knlA01 A:4-126                                                                                             --- Pfam domains
         Sec.struct. author .....ee.....eeehhhhh.......eee....hhhhh.ee.....eee...eeeee........eeeee...hhhh.eee.....eee.....eeee.hhh......eeee....hhhh.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------RICIN_B_LECTIN  PDB: A:13-129 UniProt: 361-477                                                                        PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1knl A   4 DGGQIKGVGSGRCLDVPDASTSDGTQLQLWDCHSGTNQQWAATDAGELRVYGDKCLDAAGTSNGSKVQIYSCWGGDNQKWRLNSDGSVVGVQSGLCLDAVGNGTANGTLIQLYTCSNGSNQRWTRT 129
                                    13        23        33        43        53        63        73        83        93       103       113       123      

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Trefoil (131)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XYNA_STRLI | P26514)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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
        XYNA_STRLI | P265141e0v 1e0w 1e0x 1knm 1mc9 1od8 1v0k 1v0l 1v0m 1v0n 1xas

(-) Related Entries Specified in the PDB File

1knm STREPTOMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEX WITH LACTOSE
1knn STREPROMYCES LIVIDANS XYLAN BINDING DOMAIN CBM13 IN COMPLEX WITH XYLOPENTAOSE