1OD3 - JenaLib

Title :   STRUCTURE OF CSCBM6-3 FROM CLOSTRIDIUM STERCORARIUM IN COMPLEX WITH LAMINARIBIOSE

Authors :   A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilburn, D. R. Rose, G. J. Davies

Date :   12 Feb 03 (Deposition) - 13 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Carbohydrate Binding Module, Beta-Sandwich, Laminaribiose (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. B. Boraston, V. Notenboom, R. A. J. Warren, D. G. Kilburn, D. R. Rose, G. J. Davies
Structure And Ligand Binding Of Carbohydrate-Binding Module Cscbm6-3 Reveals Similarities With Fucose-Specific Lectins And Galactose-Binding Domains
J. Mol. Biol. V. 327 659 2003
PubMed-ID: 12634060 | Reference-DOI: 10.1016/S0022-2836(03)00152-9

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:55 , TYR A:56 , PHE A:112 , ASN A:140 , BGC A:1152 , HOH A:2238 , HOH A:2255 , HOH A:2256 , HOH A:2258	BINDING SITE FOR RESIDUE BGC A1151
2	AC2	SOFTWARE	ASP A:72 , PRO A:138 , BGC A:1151 , HOH A:2259 , HOH A:2261	BINDING SITE FOR RESIDUE BGC A1152
3	AC3	SOFTWARE	GLU A:32 , ASP A:33 , TYR A:34 , ILE A:44 , ASN A:85 , VAL A:128 , BGC A:1155 , HOH A:2045 , HOH A:2263 , HOH A:2264 , HOH A:2265 , HOH A:2266 , HOH A:2267 , HOH A:2268 , HOH A:2269 , HOH A:2270	BINDING SITE FOR RESIDUE BGC A1154
4	AC4	SOFTWARE	ARG A:23 , ASP A:33 , ASP A:35 , VAL A:128 , LYS A:129 , BGC A:1154 , HOH A:2045 , HOH A:2096 , HOH A:2266 , HOH A:2271 , HOH A:2272 , HOH A:2273	BINDING SITE FOR RESIDUE BGC A1155
5	AC5	SOFTWARE	GLN A:30 , GLU A:32 , SER A:52 , ASP A:142 , HOH A:2035 , HOH A:2040	BINDING SITE FOR RESIDUE CA A1153
6	AC6	SOFTWARE	SER A:123 , ASN A:124 , HOH A:2207 , HOH A:2224 , HOH A:2251 , HOH A:2252 , HOH A:2253	BINDING SITE FOR RESIDUE ACY A1150

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:132
 aligned with XYNA1_CLOSR | Q8GJ44 from UniProtKB/Swiss-Prot  Length:651

    Alignment length:132
                                   528       538       548       558       568       578       588       598       608       618       628       638       648  
          XYNA1_CLOSR   519 VGGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSKSG 650
               SCOP domains d1od3a_ A: Putative xylanase                                                                                                         SCOP domains
               CATH domains 1od3A00 A:19-150 Galactose-binding domain-like                                                                                       CATH domains
               Pfam domains -----------CBM_6-1od3A01 A:30-148                                                                                                 -- Pfam domains
         Sec.struct. author ....ee....ee.....eee....eeee.....eeee......eeeeeeee....eeeeeeeee....eeeeeee......eeeeeee.........eeeeeeeeee..eeeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------CBM6  PDB: A:27-147 UniProt: 527-647                                                                                     --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1od3 A  19 VGGTRSAFSNIQAEDYDSSYGPNLQIFSLPGGGSAIGYIENGYSTTYKNIDFGDGATSVTARVATQNATTIQVRLGSPSGTLLGTIYVGSTGSFDTYRDVSATISNTAGVKDIVLVFSGPVNVDWFVFSKSG 150
                                    28        38        48        58        68        78        88        98       108       118       128       138       148

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (XYNA1_CLOSR | Q8GJ44)

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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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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