1OD8 - JenaLib

Title :   XYLANASE XYN10A FROM STREPTOMYCES LIVIDANS IN COMPLEX WITH XYLOBIO-ISOFAGOMINE LACTAM

Authors :   T. M. Gloster, S. Roberts, G. J. Davies

Date :   14 Feb 03 (Deposition) - 08 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase/Lectin, Glycoside Hydrolase Family 10, Xylanase, Xylan Degradation, Transition State Mimic, Isofagomine Lactam, Hydrolase, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Gloster, S. J. Williams, C. Tarling, S. Roberts, C. Dupont, P. Jodoin, F. Shareck, S. G. Withers, G. J. Davies
A Xylobiose-Derived Isofagomine Lactam Glycosidase Inhibitor Binds As Its Amide Tautomer
Chem. Commun. (Camb. ) V. 8 944 2003
PubMed-ID: 12744311 | Reference-DOI: 10.1039/B301829F

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:132 , ASN A:173 , ASN A:209 , SER A:212 , ARG A:275 , XDL A:1306 , IMD A:1309 , HOH A:2465 , HOH A:2622	BINDING SITE FOR RESIDUE XYP A1307
02	AC2	SOFTWARE	GLU A:44 , ASN A:45 , LYS A:48 , GLN A:88 , TRP A:266 , TRP A:274 , XDL A:1310 , HOH A:2624 , HOH A:2625 , HOH A:2626 , HOH A:2628 , HOH A:2629	BINDING SITE FOR RESIDUE XYP A1311
03	AC3	SOFTWARE	THR A:294 , ASP A:298 , HOH A:2303 , HOH A:2609	BINDING SITE FOR RESIDUE NA A1303
04	AC4	SOFTWARE	ASP A:298 , GLY A:302 , GLY A:303	BINDING SITE FOR RESIDUE NA A1304
05	AC5	SOFTWARE	GLU A:2 , SER A:3 , ARG A:190 , HOH A:2014	BINDING SITE FOR RESIDUE NA A1305
06	AC6	SOFTWARE	ASN A:187 , HOH A:2102 , HOH A:2438 , HOH A:2441	BINDING SITE FOR RESIDUE NA A1312
07	AC7	SOFTWARE	ASP A:132 , ASN A:173 , GLY A:211 , XYP A:1307 , HOH A:2160 , HOH A:2349 , HOH A:2619 , HOH A:2620 , HOH A:2621	BINDING SITE FOR RESIDUE XDL A1306
08	AC8	SOFTWARE	GLY A:13 , GLN A:194 , ARG A:195 , GLY A:196 , SER A:258 , CYS A:260 , LEU A:261 , HOH A:2454 , HOH A:2623	BINDING SITE FOR RESIDUE IMD A1308
09	AC9	SOFTWARE	GLU A:128 , TYR A:172 , GLN A:205 , ARG A:275 , XYP A:1307 , XDL A:1310	BINDING SITE FOR RESIDUE IMD A1309
10	BC1	SOFTWARE	LYS A:48 , HIS A:81 , TRP A:85 , ASN A:127 , GLU A:128 , GLN A:205 , GLU A:236 , TRP A:274 , IMD A:1309 , XYP A:1311	BINDING SITE FOR RESIDUE XDL A1310

SS Bonds (3, 3)

Cis Peptide Bonds (1, 1)

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)
	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:302
 aligned with XYNA_STRLI | P26514 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:302
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342  
           XYNA_STRLI    43 ESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGG 344
               SCOP domains d1od8a_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1od8A00 A:2-303 Glycosidases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --Glyco_hydro_10-1od8A01 A:4-300                                                                                                                                                                                                                                                                           --- Pfam domains
         Sec.struct. author ..hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.............hhhhhh..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh....eeee............hhhhhhhhhhh...eeeeeeeee...hhhhhhhhhhhhhh...eeeeee....hhhh.hhhhh..........hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ---------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1od8 A   2 ESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGG 303
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

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 (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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