1W32 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE 3-DIMENSIONAL STRUCTURE OF A THERMOSTABLE MUTANT OF A XYLANASE (XYN10A) FROM CELLVIBRIO JAPONICUS

Authors :   S. Andrews, E. J. Taylor, G. N. Pell, F. Vincent, V. M. A. Ducros, G. J. Davies, J. H. Lakey, H. J. Gilbert

Date :   12 Jul 04 (Deposition) - 30 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Xylanase, Mutant, Calcium Ion, Thermostable, Glycosyle Hydrolase, Family 10, Error Prone Pcr, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Andrews, E. J. Taylor, G. N. Pell, F. Vincent, V. M. A. Ducros, G. J. Davies, J. H. Lakey, H. J. Gilbert
The Use Of Forced Protein Evolution To Investigate And Improve Stability Of Family 10 Xylanases: The Production Of Ca2+-Independent Stable Xylanases
J. Biol. Chem. V. 279 54369 2004
PubMed-ID: 15452124 | Reference-DOI: 10.1074/JBC.M409044200

Molecule 1 - ENDO-1,4-BETA-XYLANASE A PRECURSOR
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-16B
	Expression System Strain	:	GM83 DE3
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 265-611
	Mutation	:	YES
	Organism Scientific	:	CELLVIBRIO JAPONICUS
	Organism Taxid	:	155077
	Other Details	:	ORGANISM FORMERLY KNOWN AS PSEUDOMONAS FLUORESCENS
	Synonym	:	XYLANASE A, 1,4-BETA-D-XYLAN XYLANOHYDROLASE A, XYLA

		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 (2, 11)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	EDO	9	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 2 (1, 7)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	EDO	7	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:253 , ASP A:256 , ASN A:258 , ASN A:261 , ASN A:262 , HOH A:2385 , HOH A:2405	BINDING SITE FOR RESIDUE CA A1347
02	AC2	SOFTWARE	ASN B:253 , ASP B:256 , ASN B:258 , ASN B:261 , ASN B:262 , HOH B:2381 , HOH B:2389 , HOH B:2398	BINDING SITE FOR RESIDUE CA B1347
03	AC3	SOFTWARE	SER A:86 , ASP A:137 , ARG A:139 , ARG A:152 , HOH A:2170 , HOH A:2508 , HOH A:2509	BINDING SITE FOR RESIDUE EDO A1348
04	AC4	SOFTWARE	ARG A:299	BINDING SITE FOR RESIDUE EDO A1349
05	AC5	SOFTWARE	PHE B:130 , ASP B:131 , SER B:132 , ALA B:188 , HOH B:2508	BINDING SITE FOR RESIDUE EDO B1348
06	AC6	SOFTWARE	ASP B:137 , ARG B:139 , ARG B:146 , GLN B:147 , HOH B:2252 , HOH B:2509 , HOH B:2510 , HOH B:2511	BINDING SITE FOR RESIDUE EDO B1349
07	AC7	SOFTWARE	ALA B:270 , VAL B:271 , LEU B:276 , ASN B:328 , HOH B:2417 , HOH B:2512	BINDING SITE FOR RESIDUE EDO B1350
08	AC8	SOFTWARE	ARG B:168 , HOH B:2514 , HOH B:2515 , HOH B:2516	BINDING SITE FOR RESIDUE EDO B1351
09	AC9	SOFTWARE	THR B:25 , SER B:26 , SER B:27 , ALA B:28 , ARG B:29 , HOH B:2045 , HOH B:2140 , HOH B:2517	BINDING SITE FOR RESIDUE EDO B1352
10	BC1	SOFTWARE	GLY B:1 , SER B:4 , TYR B:337 , HOH B:2495 , HOH B:2518	BINDING SITE FOR RESIDUE EDO B1353
11	BC2	SOFTWARE	TYR A:52 , GLY A:54 , PRO A:90 , ASN A:91 , TRP A:92 , HOH B:2391 , HOH B:2519	BINDING SITE FOR RESIDUE EDO B1354

Asymmetric Unit

No.	Residues
1	A:269	-	A:273
2	A:269	-	A:273
3	B:269	-	B:273

Asymmetric Unit

No.	Residues
1	His A:79	-	Ala A:80
2	Tyr A:220	-	Pro A:221
3	Tyr B:220	-	Pro B:221

(no "SAP(SNP)/Variant" information available for 1W32)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_2	PS51760	Glycosyl hydrolases family 10 (GH10) domain profile.	XYNA_CELJU	281-607	2	A:17-343 B:17-343
2	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_CELJU	503-513	2	A:239-249 B:239-249

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_2	PS51760	Glycosyl hydrolases family 10 (GH10) domain profile.	XYNA_CELJU	281-607	1	A:17-343 -
2	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_CELJU	503-513	1	A:239-249 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GH10_2	PS51760	Glycosyl hydrolases family 10 (GH10) domain profile.	XYNA_CELJU	281-607	1	- B:17-343
2	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_CELJU	503-513	1	- B:239-249

(no "Exon" information available for 1W32)

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:346
 aligned with XYNA_CELJU | P14768 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:346
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      
           XYNA_CELJU   265 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 610
               SCOP domains d1w32a_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w32A00 A:1-346 Glycosidases                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh...eeeee...........hhhhhhhhhhhh.eeee....hhhh.ee..ee.hhhhhhhhhhhhhh..eeeeeeee..hhhhh.........hhhhhhhhhhhhhhhhh.....eeeeee....hhhhh.....ee..ee.hhhhhhhh.hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh.....eeeeeeeeee..............hhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhh...ee..ee............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------GH10_2  PDB: A:17-343 UniProt: 281-607                                                                                                                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w32 A   1 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNNYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 346
                                    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       320       330       340

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with XYNA_CELJU | P14768 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:346
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604      
           XYNA_CELJU   265 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 610
               SCOP domains d1w32b_ B: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1w32B00 B:1-346 Glycosidases                                                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) Glyco_hydro_10-1w32B01 B:1-344                                                                                                                                                                                                                                                                                                                          -- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_10-1w32B02 B:1-344                                                                                                                                                                                                                                                                                                                          -- Pfam domains (2)
         Sec.struct. author hhhhhh...eeeee...........hhhhhhhhhhhh.eeee....hhhh.ee..ee.hhhhhhhhhhhhhh..eeeeeeee..hhhhh.........hhhhhhhhhhhhhhhhh.....eeeeee..............ee..ee.hhhhhhhh.hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh.....eeeeeeeeee......................hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhh...ee..ee............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------GH10_2  PDB: B:17-343 UniProt: 281-607                                                                                                                                                                                                                                                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     ------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w32 B   1 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNNYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 346
                                    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       320       330       340

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(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

Pseudomonas fluorescens [TaxId: 294] (7)

1a	d1w32a_	A:
1b	d1w32b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Cellvibrio japonicus. Organism_taxid: 155077. (10)

1a	1w32A00	A:1-346
1b	1w32B00	B:1-346

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_10 (42)

Cellvibrio japonicus (strain Ueda107) (Pseudomonas fluorescens subsp. cellulosa) (4)

1a	Glyco_hydro_10-1w32B01	B:1-344
1b	Glyco_hydro_10-1w32B02	B:1-344

Asymmetric Unit(hide GO term definitions)

Chain A,B (XYNA_CELJU | P14768)

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:0030248	cellulose binding	Interacting selectively and non-covalently with cellulose.
	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.
	GO:0030247	polysaccharide binding	Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		His A:79 - Ala A:80	[ RasMol ]
		Tyr A:220 - Pro A:221	[ RasMol ]
		Tyr B:220 - Pro B:221	[ RasMol ]

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	1w32
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	XYNA_CELJU \| P14768
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UniProtKB/Swiss-Prot
	XYNA_CELJU \| P14768	:	1clx 1e5n 1e8r 1qld 1w2p 1w2v 1w3h 1xys

1clx	CATALYTIC CORE OF XYLANASE A
1e5n	E246C MUTANT OF P FLUORESCENS SUBSP. CELLULOSA XYLANASE A IN COMPLEX WITH XYLOPENTAOSE
1e8r	SOLUTION STRUCTURE OF TYPE X CBD
1qld	SOLUTION STRUCTURE OF TYPE X CBM
1w2p	THE 3-DIMENSIONAL STRUCTURE OF A XYLANASE ( XYN10A) FROM CELLVIBRIO JAPONICUS
1w2v	THE 3-DIMENSIONAL STRUCTURE OF A THERMOSTABLE MUTANT OF A XYLANASE (XYN10A) FROM CELLVIBRIO JAPONICUS
1w3h	THE 3-DIMENSIONAL STRUCTURE OF A THERMOSTABLE MUTANT OF A XYLANASE (XYN10A) FROM CELLVIBRIO JAPONICUS
1xys	CATALYTIC CORE OF XYLANASE A E246C MUTANT

Description

Compounds

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Ligands, Modified Residues, Ions (2, 11)

Sites (11, 11)

SS Bonds (3, 3)

Cis Peptide Bonds (3, 3)

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SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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