1RED - JenaLib

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Title :   ENDO-1,4-BETA-XYLANASE II COMPLEX WITH 4,5-EPOXYPENTYL-BETA-D-XYLOSIDE

Authors :   J. Rouvinen, R. Havukainen, A. Torronen

Date :   21 Dec 95 (Deposition) - 11 Jan 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

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

Reference :   R. Havukainen, A. Torronen, T. Laitinen, J. Rouvinen
Covalent Binding Of Three Epoxyalkyl Xylosides To The Active Site Of Endo-1, 4-Xylanase Ii From Trichoderma Reesei.
Biochemistry V. 35 9617 1996
PubMed-ID: 8755744 | Reference-DOI: 10.1021/BI953052N
(for further references see the PDB file header)

Molecule 1 - ENDO-1,4-BETA-XYLANASE II
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Organism Scientific	:	HYPOCREA JECORINA
	Organism Taxid	:	51453
	Strain	:	TRICHODERMA REESEI RUT-C30
	Synonym	:	XYNII

		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, 4)

No.	Name	Count	Type	Full Name
1	BEZ	1	Ligand/Ion	BENZOIC ACID
2	C5X	1	Ligand/Ion	4,5-EPOXYPENTYL-BETA-D-XYLOSIDE
3	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BEZ	-1	Ligand/Ion	BENZOIC ACID
2	C5X	-1	Ligand/Ion	4,5-EPOXYPENTYL-BETA-D-XYLOSIDE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	BEZ	1	Ligand/Ion	BENZOIC ACID
2	C5X	1	Ligand/Ion	4,5-EPOXYPENTYL-BETA-D-XYLOSIDE
3	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:18 , VAL B:46 , TYR B:77 , GLU B:86 , TYR B:88 , SER B:127 , TYR B:171 , GLU B:177 , HOH B:691 , HOH B:778	BINDING SITE FOR RESIDUE C5X B 401
2	AC2	SOFTWARE	LYS A:104 , GLY A:106 , THR B:2	BINDING SITE FOR RESIDUE BEZ B 402

(no "SS Bond" information available for 1RED)

Asymmetric Unit

No.	Residues
1	Gln A:52	-	Pro A:53
2	Asn A:82	-	Pro A:83
3	Gln B:52	-	Pro B:53
4	Asn B:82	-	Pro B:83

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_3	PS51761	Glycosyl hydrolases family 11 (GH11) domain profile.	XYN2_HYPJR	34-223	2	A:2-190 B:2-190
2	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYN2_HYPJR	116-126	2	A:83-93 B:83-93
3	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYN2_HYPJR	207-218	2	A:174-185 B:174-185

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_3	PS51761	Glycosyl hydrolases family 11 (GH11) domain profile.	XYN2_HYPJR	34-223	1	A:2-190 -
2	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYN2_HYPJR	116-126	1	A:83-93 -
3	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYN2_HYPJR	207-218	1	A:174-185 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_3	PS51761	Glycosyl hydrolases family 11 (GH11) domain profile.	XYN2_HYPJR	34-223	1	- B:2-190
2	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYN2_HYPJR	116-126	1	- B:83-93
3	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYN2_HYPJR	207-218	1	- B:174-185

(no "Exon" information available for 1RED)

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
	(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:190
 aligned with XYN2_HYPJR | P36217 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:190
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
           XYN2_HYPJR    34 QTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 223
               SCOP domains d1reda_ A: Xylanase II                                                                                                                                                                         SCOP domains
               CATH domains -1redA00 A:2-190  [code=2.60.120.180, no name defined]                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeee...........eeeeeeee......eeeehhhhhhhhhhh.........eeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GH11_3  PDB: A:2-190 UniProt: 34-223                                                                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1red A   1 xTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
                            |                                                                                                                                                                                             
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with XYN2_HYPJR | P36217 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:190
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
           XYN2_HYPJR    34 QTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 223
               SCOP domains d1redb_ B: Xylanase II                                                                                                                                                                         SCOP domains
               CATH domains -1redB00 B:2-190  [code=2.60.120.180, no name defined]                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..eeeeeee.....eeeee....eeeeee....eeeeeeee.......eeeeeeeeeee..eeeeeeeee....eeeeeeeee.........eeeeeeee..eeeeeeeeee...........eeeeeeee......eeeehhhhhhhhhhh.........eeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) GH11_3  PDB: B:2-190 UniProt: 34-223                                                                                                                                                           PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1red B   1 xTIQPGTGYNNGYFYSYWNDGHGGVTYTNGPGGQFSVNWSNSGNFVGGKGWQPGTKNKVINFSGSYNPNGNSYLSVYGWSRNPLIEYYIVENFGTYNPSTGATKLGEVTSDGSVYDIYRTQRVNQPSIIGTATFYQYWSVRRNHRSSGSVNTANHFNAWAQQGLTLGTMDYQIVAVEGYFSSGSASITVS 190
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
                            1-PCA

Legend:		→ Mismatch	(orange background)
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	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( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Xylanase/endoglucanase 11/12 (93)

Protein domain: Xylanase II (65)

Trichoderma reesei, xynII [TaxId: 51453] (12)

1a	d1reda_	A:
1b	d1redb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.180, no name defined] (77)

Hypocrea jecorina. Organism_taxid: 51453. Strain: trichoderma reesei rut-c30 (3)

1a	1redA00	A:2-190
1b	1redB00	B:2-190

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYN2_HYPJR | P36217)

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.

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