1E0X - JenaLib

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Title :   XYLANASE 10A FROM SREPTOMYCES LIVIDANS. XYLOBIOSYL-ENZYME INTERMEDIATE AT 1.65 A

Authors :   V. Ducros, S. J. Charnock, U. Derewenda, Z. S. Derewenda, Z. Dauter, C. Dupont, F. Shareck, R. Morosoli, D. Kluepfel, G. J. Davies

Date :   10 Apr 00 (Deposition) - 05 Apr 01 (Release) - 31 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Glycoside Hydrolase Family 10, Hydrolase, Xylan Degradation, Glycosyl-Enzyme Intermediate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Ducros, S. J. Charnock, U. Derewenda, Z. S. Derewenda, Z. Dauter, C. Dupont, F. Shareck, R. Morosoli, D. Kluepfel, G. J. Davies
Substrate Specificity In Glycoside Hydrolase Family 10. Structural And Kinetic Analysis Of The Streptomyces Lividans Xylanase 10A
J. Biol. Chem. V. 275 23020 2000
PubMed-ID: 10930426 | Reference-DOI: 10.1074/JBC.M000129200
(for further references see the PDB file header)

Molecule 1 - ENDO-1,4-BETA-XYLANASE A
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	STREPTOMYCES LIVIDANS
	Expression System Strain	:	IAF 19
	Expression System Taxid	:	1916
	Fragment	:	CATALYTIC MODULE, RESIDUES 32-450
	Organism Scientific	:	STREPTOMYCES LIVIDANS
	Organism Taxid	:	1916
	Other Details	:	GLYCOSYL ENXYME INTERMEDIATE. COVALENT LINK BETWEEN GLU 236 AND THE SUBSTRATE
	Synonym	:	XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	X2F	2	Ligand/Ion	2-DEOXY-2-FLUORO XYLOPYRANOSE
3	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	X2F	1	Ligand/Ion	2-DEOXY-2-FLUORO XYLOPYRANOSE
3	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	X2F	1	Ligand/Ion	2-DEOXY-2-FLUORO XYLOPYRANOSE
3	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:73 , HOH A:2361 , HOH A:2362 , HOH A:2363	BINDING SITE FOR RESIDUE GOL A 400
2	AC2	SOFTWARE	HIS A:86 , GLN A:89 , GLN A:94 , SER A:141 , ASN A:142 , HOH A:2364 , HOH A:2365 , HOH A:2366	BINDING SITE FOR RESIDUE GOL A 401
3	AC3	SOFTWARE	TYR B:68 , ASN B:69 , VAL B:72 , GLN B:73 , HOH B:2345	BINDING SITE FOR RESIDUE GOL B 400
4	AC4	SOFTWARE	GLU A:44 , ASN A:45 , LYS A:48 , HIS A:81 , TRP A:85 , GLN A:88 , ASN A:127 , GLN A:205 , HIS A:207 , GLU A:236 , TRP A:266 , TRP A:274 , HOH A:2367 , HOH A:2368 , HOH A:2369	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 701 TO 702
5	AC5	SOFTWARE	GLU B:44 , ASN B:45 , LYS B:48 , HIS B:81 , TRP B:85 , GLN B:88 , ASN B:127 , GLN B:205 , HIS B:207 , GLU B:236 , TRP B:266 , TRP B:274 , HOH B:2346 , HOH B:2347 , HOH B:2348	BINDING SITE FOR CHAIN B OF DI-SACCHARIDE X2F B 701 AND XYP B 702

Asymmetric Unit

No.	Residues
1	A:168	-	A:201
2	A:168	-	A:201
3	A:254	-	A:260
4	B:168	-	B:201
5	B:168	-	B:201
6	B:254	-	B:260

Asymmetric Unit

No.	Residues
1	His A:81	-	Thr A:82
2	His B:81	-	Thr B:82

(no "SAP(SNP)/Variant" information available for 1E0X)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_STRLI	270-280	2	A:229-239 B:229-239

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_STRLI	270-280	1	A:229-239 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_STRLI	270-280	1	- B:229-239

(no "Exon" information available for 1E0X)

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
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Chain A from PDB  Type:PROTEIN  Length:310
 aligned with XYNA_STRLI | P26514 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:310
                                    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       311       321       331       341       351
           XYNA_STRLI    42 AESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGGDSSEPPA 351
               SCOP domains d1e0xa_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1e0xA00 A:1-309 Glycosidases                                                                                                                                                                                                                                                                                         - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eee..........hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.............hhhhhh..hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh....eeee............hhhhhhhhhhh...eeee........hhhhhhhhhhhhhh.....eeee....hhhh.hhhhh..........hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e0x A   1 AESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGGDSSEPPA 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with XYNA_STRLI | P26514 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:310
                                    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       311       321       331       341       351
           XYNA_STRLI    42 AESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGGDSSEPPA 351
               SCOP domains d1e0xb_ B: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1e0xB00 B:1-309 Glycosidases                                                                                                                                                                                                                                                                                         - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeehhhhh.hhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eee..........hhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeeee.............hhhhhhh.hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhhhhhh....eeee............hhhhhhhhhhh...eeee........hhhhhhhhhhhhhh.....eeee....hhhh.hhhhh..........hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ----------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e0x B   1 AESTLGAAAAQSGRYFGTAIASGRLSDSTYTSIAGREFNMVTAENEMKIDATEPQRGQFNFSSADRVYNWAVQNGKQVRGHTLAWHSQQPGWMQSLSGSALRQAMIDHINGVMAHYKGKIVQWDVVNEAFADGSSGARRDSNLQRSGNDWIEVAFRTARAADPSAKLCYNDYNVENWTWAKTQAMYNMVRDFKQRGVPIDCVGFQSHFNSGSPYNSNFRTTLQNFAALGVDVAITELDIQGAPASTYANVTNDCLAVSRCLGITVWGVRDSDSWRSEQTPLLFNNDGSKKAAYTAVLDALNGGDSSEPPA 310
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: (Trans)glycosidases (1191)

Family: beta-glycanases (284)

Protein domain: Xylanase A, catalytic core (61)

Streptomyces lividans [TaxId: 1916] (9)

1a	d1e0xa_	A:
1b	d1e0xb_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Streptomyces lividans. Organism_taxid: 1916. (8)

1a	1e0xA00	A:1-309
1b	1e0xB00	B:1-309

(no "Pfam Domain" information available for 1E0X)

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	XYNA_STRLI \| P26514	:	1e0v 1e0w 1knl 1knm 1mc9 1od8 1v0k 1v0l 1v0m 1v0n 1xas

1e0v	XYLANASE 10A FROM SREPTOMYCES LIVIDANS. CELLOBIOSYL-ENZYME INTERMEDIATE AT 1.7 A
1e0w	XYLANASE 10A FROM SREPTOMYCES LIVIDANS. NATIVE STRUCTURE AT 1.2 ANGSTROM RESOLUTION
1xas	XYLANASE A

Description

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Ligands, Modified Residues, Ions (3, 7)

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SS Bonds (6, 6)

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