1UR1 - JenaLib

Title :   XYLANASE XYN10B MUTANT (E262S) FROM CELLVIBRIO MIXTUS IN COMPLEX WITH ARABINOFURANOSE ALPHA-1,3 LINKED TO XYLOBIOSE

Authors :   G. Pell, E. J. Taylor, T. M. Gloster, J. P. Turkenburg, C. M. G. A. Fontes, L. M. A. Ferreira, G. J. Davies, H. J. Gilbert

Date :   24 Oct 03 (Deposition) - 18 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.43

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Family 10, Xylanase, Glycoside Hydrolase, Hemicellulose, Xylan Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Pell, E. J. Taylor, T. M. Gloster, J. P. Turkenburg, C. M. G. A. Fontes, L. M. A. Ferreira, T. Nagy, S. Clark, G. J. Davies, H. J. Gilbert
The Mechanisms By Which Family 10 Glycoside Hydrolases Bind Decorated Substrates
J. Biol. Chem. V. 279 9597 2004
PubMed-ID: 14668328 | Reference-DOI: 10.1074/JBC.M312278200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:71 , HIS A:104 , TRP A:108 , ASN A:156 , GLN A:231 , HIS A:233 , SER A:262 , TRP A:328 , TRP A:336 , XYP A:1377 , HOH A:2446 , HOH A:2561	BINDING SITE FOR RESIDUE XYS A1376
2	AC2	SOFTWARE	GLU A:67 , ASN A:68 , LYS A:71 , GLN A:111 , TRP A:328 , TRP A:336 , XYS A:1376 , AHR A:1378 , HOH A:2562 , HOH A:2563 , HOH A:2564	BINDING SITE FOR RESIDUE XYP A1377
3	AC3	SOFTWARE	GLU A:67 , ASN A:68 , ALA A:334 , XYP A:1377 , HOH A:2104 , HOH A:2563 , HOH A:2565 , HOH A:2566 , HOH A:2567 , HOH A:2568	BINDING SITE FOR RESIDUE AHR A1378
4	AC4	SOFTWARE	ALA A:43 , ASN A:68 , HOH A:2074	BINDING SITE FOR RESIDUE CL A1379
5	AC5	SOFTWARE	HOH A:2078 , HOH A:2079 , HOH A:2083 , HOH A:2183 , HOH A:2314 , HOH A:2317	BINDING SITE FOR RESIDUE MG A1380

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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:346
 aligned with O68541_9GAMM | O68541 from UniProtKB/TrEMBL  Length:379

    Alignment length:350
                                                                                                                                                                                                                                                                                                                                                                                  379     
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374    |    -
         O68541_9GAMM    35 GLKSAYKDNFLIGAALNATIASGADERLNTLIAKEFNSITPENCMKWGVLRDAQGQWNWKDADAFVAFGTKHNLHMVGHTLVWHSQIHDEVFKNADGSYISKAALQKKMEEHITTLAGRYKGKLAAWDVVNEAVGDDLKMRDSHWYKIMGDDFIYNAFTLANEVDPKAHLMYNDYNIERTGKREATVEMIERLQKRGMPIHGLGIQGHLGIDTPPIAEIEKSIIAFAKLGLRVHFTELDVDVLPSVWELPVAEVSTRFEYKPERDPYTKGLPQEMQDKLAKRYEDLFKLFIKHSDKIDRATFWGVSDDASWLNGFPIPGRTNYPLLFDRKLQPKDAYFRLLDLKR-----   -
               SCOP domains d1ur1a_ A: Xylanase                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1ur1A00 A:26-375 Glycosidases                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains Glyco_hydro_10-1ur1A01 A:26-369                                                                                                                                                                                                                                                                                                                         ------ Pfam domains
         Sec.struct. author hhhhhh....eeeeeehhhhhh..hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeeeeeee.....hhhhh........hhhhhhhhhhhhhhhhhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh...eeeeeeeeee.......----........hhhhh......hhhhhhhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhh...................hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur1 A  26 GLKSAYKDNFLIGAALNATIASGADERLNTLIAKEFNSITPENCMKWGVLRDAQGQWNWKDADAFVAFGTKHNLHMVGHTLVWHSQIHDEVFKNADGSYISKAALQKKMEEHITTLAGRYKGKLAAWDVVNEAVGDDLKMRDSHWYKIMGDDFIYNAFTLANEVDPKAHLMYNDYNIERTGKREATVEMIERLQKRGMPIHGLGIQGHLGIDTPPIAEIEKSIIAFAKLGLRVHFTSLDVDVLPSVWE----EVSTRFEYKPERDPYTKGLPQEMQDKLAKRYEDLFKLFIKHSDKIDRATFWGVSDDASWLNGFPIPGRTNYPLLFDRKLQPKDAYFRLLDLKRLEHHH 375
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       | -  |    285       295       305       315       325       335       345       355       365       375
                                                                                                                                                                                                                                                                                 273  278

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 (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (O68541_9GAMM | O68541)

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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		AHR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		XYP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		XYS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		His A:104 - Thr A:105	[ RasMol ]
		Phe A:340 - Pro A:341	[ RasMol ]
		Thr A:238 - Pro A:239	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1ur1
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	O68541_9GAMM \| O68541
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	3.2.1.8
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description