3VZN - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE BACILLUS CIRCULANS ENDO-BETA-(1,4)-XYLANASE (BCX) N35E MUTANT WITH GLU78 COVALENTLY BONDED TO 2-DEOXY-2-FLUORO-XYLOBIOSE

Authors :   M. L. Ludwiczek, I. D'Angelo, G. N. Yalloway, M. Okon, J. E. Nielsen, N. C. Strynadka, S. G. Withers, L. P. Mcintosh

Date :   15 Oct 12 (Deposition) - 08 May 13 (Release) - 31 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.67

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

Keywords :   Xylanase, Gh-11 Glycoside Hydrolase, Glycosyl-Enzyme Intermediate, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. L. Ludwiczek, I. D'Angelo, G. N. Yalloway, J. A. Brockerman, M. Okon J. E. Nielsen, N. C. Strynadka, S. G. Withers, L. P. Mcintosh
Strategies For Modulating The Ph-Dependent Activity Of A Family 11 Glycoside Hydrolase
Biochemistry V. 52 3138 2013
PubMed-ID: 23578322 | Reference-DOI: 10.1021/BI400034M

Molecule 1 - ENDO-1,4-BETA-XYLANASE
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	XLNA
	Mutation	:	YES
	Organism Scientific	:	BACILLUS CIRCULANS
	Organism Taxid	:	1397
	Synonym	:	XYLANASE, 1,4-BETA-D-XYLAN XYLANOHYDROLASE

		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	DFX	2	Ligand/Ion	1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
2	SO4	3	Ligand/Ion	SULFATE ION
3	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DFX	1	Ligand/Ion	1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
2	SO4	-1	Ligand/Ion	SULFATE ION
3	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	DFX	1	Ligand/Ion	1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
2	SO4	3	Ligand/Ion	SULFATE ION
3	XYP	1	Ligand/Ion	BETA-D-XYLOPYRANOSE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:61 , SER B:177 , HOH B:310 , HOH B:329 , HOH B:383	BINDING SITE FOR RESIDUE SO4 B 203
2	AC2	SOFTWARE	ALA A:1 , SER B:100 , ASP B:101 , ASN B:148	BINDING SITE FOR RESIDUE SO4 B 204
3	AC3	SOFTWARE	ARG B:112 , TYR B:113 , HOH B:384	BINDING SITE FOR RESIDUE SO4 B 205
4	AC4	SOFTWARE	GLN A:7 , TRP A:9 , GLU A:35 , TYR A:69 , TRP A:71 , GLU A:78 , TYR A:80 , ARG A:112 , PRO A:116 , SER A:117 , PHE A:125 , GLN A:127 , TYR A:166 , HOH A:391	BINDING SITE FOR LINKED RESIDUES A 201 to 202
5	AC5	SOFTWARE	GLN B:7 , GLU B:35 , TYR B:69 , TRP B:71 , GLU B:78 , TYR B:80 , ARG B:112 , PRO B:116 , PHE B:125 , GLN B:127 , TYR B:166	BINDING SITE FOR LINKED RESIDUES B 201 to 202

(no "SS Bond" information available for 3VZN)

Asymmetric Unit

No.	Residues
1	Ser A:74	-	Pro A:75
2	Ser B:74	-	Pro B:75

(no "SAP(SNP)/Variant" information available for 3VZN)

Asymmetric Unit (2, 4)

	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_BACCI	103-113	2	A:75-85 B:75-85
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_BACCI	197-208	2	A:169-180 B:169-180

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_BACCI	103-113	1	A:75-85 -
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_BACCI	197-208	1	A:169-180 -

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_BACCI	103-113	1	- B:75-85
2	GH11_2	PS00777	Glycosyl hydrolases family 11 (GH11) active site signature 2.	XYNA_BACCI	197-208	1	- B:169-180

(no "Exon" information available for 3VZN)

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:185
 aligned with XYNA_BACCI | P09850 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:185
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     
           XYNA_BACCI    29 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d3vzna_ A: Xylanase II                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeee..eeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeeeeeee.........eeeehhhhhhhhhhh......eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzn A   1 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGEFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with XYNA_BACCI | P09850 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:185
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208     
           XYNA_BACCI    29 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 213
               SCOP domains d3vznb_ B: Xylanase II                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee....eeeeee....eeeeeee...eeeeeeee.......eeeeeeeeeeee..eeeeeeeeee...eeeeeeeee.......eeeeeeee..eeeeeeeeeeeee.......eeeeeeeeee.........eeeehhhhhhhhhhh......eeeeeeeeeeee..eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------GH11_1     -----------------------------------------------------------------------------------GH11_2      ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzn B   1 ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGEFVVGKGWTTGSPFRTINYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKSDGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHVNAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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)

Bacillus circulans [TaxId: 1397] (21)

1a	d3vzna_	A:
1b	d3vznb_	B:

(no "CATH Domain" information available for 3VZN)

(no "Pfam Domain" information available for 3VZN)

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYNA_BACCI | P09850)

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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	Cis Peptide Bonds
		Ser A:74 - Pro A:75	[ RasMol ]
		Ser B:74 - Pro B:75	[ RasMol ]

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	3vzn
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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Gene Ontology (8, 8)

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