1UKR - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF ENDO-1,4-BETA-XYLANASE C

Authors :   U. Krengel, B. W. Dijkstra

Date :   23 Aug 96 (Deposition) - 24 Dec 97 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

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

Reference :   U. Krengel, B. W. Dijkstra
Three-Dimensional Structure Of Endo-1, 4-Beta-Xylanase I From Aspergillus Niger: Molecular Basis For Its Low Ph Optimum.
J. Mol. Biol. V. 263 70 1996
PubMed-ID: 8890913 | Reference-DOI: 10.1006/JMBI.1996.0556
(for further references see the PDB file header)

Molecule 1 - ENDO-1,4-B-XYLANASE I
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ASPERGILLUS NIGER
	Organism Taxid	:	5061
	Synonym	:	XYLANASE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1UKR)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	EA	UNKNOWN	GLU A:79 , GLU A:170	GLU A 79 AND GLU A 170 REFER TO THE CATALYTIC ACIDIC RESIDUES.
2	EB	UNKNOWN	GLU B:79 , GLU B:170	GLU B 79 AND GLU B 170 REFER TO THE CATALYTIC ACIDIC RESIDUES.
3	EC	UNKNOWN	GLU C:79 , GLU C:170	GLU C 79 AND GLU C 170 REFER TO THE CATALYTIC ACIDIC RESIDUES.
4	ED	UNKNOWN	GLU D:79 , GLU D:170	GLU D 79 AND GLU D 170 REFER TO THE CATALYTIC ACIDIC RESIDUES.

Asymmetric Unit

No.	Residues
1	A:92	-	A:111
2	B:92	-	B:111
3	C:92	-	C:111
4	D:92	-	D:111

Asymmetric Unit

No.	Residues
1	Tyr A:75	-	Pro A:76
2	Tyr B:75	-	Pro B:76
3	Tyr C:75	-	Pro C:76
4	Tyr D:75	-	Pro D:76

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

Asymmetric Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYNA_ASPNG	103-113	4	A:76-86 B:76-86 C:76-86 D:76-86
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_ASPNG	194-205	4	A:168-178 B:168-178 C:168-178 D:168-178

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYNA_ASPNG	103-113	1	A:76-86 - - -
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_ASPNG	194-205	1	A:168-178 - - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYNA_ASPNG	103-113	1	- B:76-86 - -
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_ASPNG	194-205	1	- B:168-178 - -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYNA_ASPNG	103-113	1	- - C:76-86 -
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_ASPNG	194-205	1	- - C:168-178 -

Biological Unit 4 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH11_1	PS00776	Glycosyl hydrolases family 11 (GH11) active site signature 1.	XYNA_ASPNG	103-113	1	- - - D:76-86
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_ASPNG	194-205	1	- - - D:168-178

(no "Exon" information available for 1UKR)

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:181
 aligned with XYNA_ASPNG | P55329 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:181
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           XYNA_ASPNG    30 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVMAVEAWSGAGSASVTIS 210
               SCOP domains d1ukra_ A: Xylanase II                                                                                                                                                                SCOP domains
               CATH domains 1ukrA00 A:3-183  [code=2.60.120.180, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhh.eeeee....eeeee........eeeeeee.......eeeeeeee....eeeeeeeeee....eeeeeeeee....hhhh.eeeeeeee..eeeeeeeeee..eee..eee.eeeeeeee.....eeee.hhhhhhhhhhh.........eeeeeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ukr A   3 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSASYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAHHGFGNSDFNYQVVAVEAWSGAGSASVTIS 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with XYNA_ASPNG | P55329 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:181
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           XYNA_ASPNG    30 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVMAVEAWSGAGSASVTIS 210
               SCOP domains d1ukrb_ B: Xylanase II                                                                                                                                                                SCOP domains
               CATH domains 1ukrB00 B:3-183  [code=2.60.120.180, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhh.eeeee....eeeee........eeeeeee.......eeeeeeee.....eeeeeeeee....eeeeeeeee....hhh..eeeeeeee..eeeeeeeeee..eee..eee.eeeeeeee.....eeee.hhhhhhhhhhh.........eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ukr B   3 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSASYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAHHGFGNSDFNYQVVAVEAWSGAGSASVTIS 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain C from PDB  Type:PROTEIN  Length:181
 aligned with XYNA_ASPNG | P55329 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:181
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           XYNA_ASPNG    30 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVMAVEAWSGAGSASVTIS 210
               SCOP domains d1ukrc_ C: Xylanase II                                                                                                                                                                SCOP domains
               CATH domains 1ukrC00 C:3-183  [code=2.60.120.180, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhh.eeeee....eeeee........eeeeeee.......eeeeeeee....eeeeeeeeee....eeeeeeeee....hhhh.eeeeeeee..eeeeeeeeee..eee..eee.eeeeeeee.....eeee.hhhhhhhhhhh.........eeeeeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ukr C   3 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSASYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAHHGFGNSDFNYQVVAVEAWSGAGSASVTIS 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Chain D from PDB  Type:PROTEIN  Length:181
 aligned with XYNA_ASPNG | P55329 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:181
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209 
           XYNA_ASPNG    30 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSKAITYSAEYSASGSSSYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAQHGFGNSDFNYQVMAVEAWSGAGSASVTIS 210
               SCOP domains d1ukrd_ D: Xylanase II                                                                                                                                                                SCOP domains
               CATH domains 1ukrD00 D:3-183  [code=2.60.120.180, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) Glyco_hydro_11-1ukrD01 D:3-182                                                                                                                                                      - Pfam domains (1)
           Pfam domains (2) Glyco_hydro_11-1ukrD02 D:3-182                                                                                                                                                      - Pfam domains (2)
           Pfam domains (3) Glyco_hydro_11-1ukrD03 D:3-182                                                                                                                                                      - Pfam domains (3)
           Pfam domains (4) Glyco_hydro_11-1ukrD04 D:3-182                                                                                                                                                      - Pfam domains (4)
         Sec.struct. author ...eeeee.hhh.eeeee....eeeee........eeeeeee.......eeeeeeee....eeeeeeeeee....eeeeeeeee....hhhh.eeeeeeee..eeeeeeeeee..eee..eee.eeeeeeee.....eeee.hhhhhhhhhhh.........eeeeeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------GH11_1     --------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ukr D   3 GINYVQNYNGNLGDFTYDESAGTFSMYWEDGVSSDFVVGLGWTTGSSNAITYSAEYSASGSASYLAVYGWVNYPQAEYYIVEDYGDYNPCSSATSLGTVYSDGSTYQVCTDTRTNEPSITGTSTFTQYFSVRESTRTSGTVTVANHFNFWAHHGFGNSDFNYQVVAVEAWSGAGSASVTIS 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Aspergillus niger [TaxId: 5061] (1)

1a	d1ukra_	A:
1b	d1ukrb_	B:
1c	d1ukrc_	C:
1d	d1ukrd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

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

Aspergillus niger. Organism_taxid: 5061. (2)

1a	1ukrA00	A:3-183
1b	1ukrB00	B:3-183
1c	1ukrC00	C:3-183
1d	1ukrD00	D:3-183

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Concanavalin (293)

Family: Glyco_hydro_11 (14)

Aspergillus niger (2)

1a	Glyco_hydro_11-1ukrD01	D:3-182
1b	Glyco_hydro_11-1ukrD02	D:3-182
1c	Glyco_hydro_11-1ukrD03	D:3-182
1d	Glyco_hydro_11-1ukrD04	D:3-182

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (XYNA_ASPNG | P55329)

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.
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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	Cis Peptide Bonds
		Tyr A:75 - Pro A:76	[ RasMol ]
		Tyr B:75 - Pro B:76	[ RasMol ]
		Tyr C:75 - Pro C:76	[ RasMol ]
		Tyr D:75 - Pro D:76	[ RasMol ]

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	XYNA_ASPNG \| P55329	:	1t6g 2qz2

(no "Related Entries Specified in the PDB File" available for 1UKR)

Description

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Ligands, Modified Residues, Ions (0, 0)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

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