1W3H - 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. Glbert

Date :   15 Jul 04 (Deposition) - 30 Sep 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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

Keywords :   Xylanase, Calcium Ion, Thermostable, Glycosyle Hydrolase, Family 10, Error Prone Pcr, Hydrolase, Treble Mutant, (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 Taxid	:	562
	Expression System Vector	:	PET-16B
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 265-611
	Mutation	:	YES
	Organism Scientific	:	CELLVIBRIO JAPONICUS
	Organism Taxid	:	155077
	Strain	:	GM83 DE3
	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, 4)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:253 , ASP A:256 , ASN A:258 , ASN A:261 , ASN A:262 , HOH A:2251 , HOH A:2252	BINDING SITE FOR RESIDUE CA A1347
2	AC2	SOFTWARE	ASN B:253 , ASP B:256 , ASN B:258 , ASN B:261 , ASN B:262 , HOH B:2239 , HOH B:2248	BINDING SITE FOR RESIDUE CA B1348
3	AC3	SOFTWARE	HIS A:84 , ASP A:134 , ARG A:146 , SER A:148 , HOH A:2043 , HOH A:2307 , HOH A:2308	BINDING SITE FOR RESIDUE EDO A1348
4	AC4	SOFTWARE	HIS B:84 , ASP B:134 , ARG B:146 , SER B:148 , HOH B:2153 , HOH B:2319	BINDING SITE FOR RESIDUE EDO B1349

Asymmetric Unit

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 1W3H)

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 1W3H)

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:348
 aligned with XYNA_CELJU | P14768 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:348
                                   272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602        
           XYNA_CELJU   263 GNGLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 610
               SCOP domains d1w3ha_ A: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1w3hA00 A:-1-346 Glycosidases                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhh...eeeee...........hhhhhhhhhhhh.eeee.....hhh.ee..ee.hhhhhhhhhhhhhh..eeeeeeee..hhhhh.........hhhhhhhhhhhhhhhhh.....eeeeee....hhhhh............hhhhhhhh.hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh.....eeeeeeeeee..hhhhh...............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
                 1w3h A  -1 SPGLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHTLVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNNYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSG 346
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338

Chain B from PDB  Type:PROTEIN  Length:347
 aligned with XYNA_CELJU | P14768 from UniProtKB/Swiss-Prot  Length:611

    Alignment length:347
                                   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 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHALVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNDYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSGR 611
               SCOP domains d1w3hb_ B: Xylanase A, catalytic core                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1w3hB00 B:1-347 Glycosidases                                                                                                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) Glyco_hydro_10-1w3hB01 B:1-344                                                                                                                                                                                                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) Glyco_hydro_10-1w3hB02 B:1-344                                                                                                                                                                                                                                                                                                                          --- Pfam domains (2)
         Sec.struct. author hhhhhh...eeeee...........hhhhhhhhhhhh.eeee....hhhh.ee..ee.hhhhhhhhhhhhhh..eeeeeeee..hhhhh.........hhhhhhhhhhhhhhhhh.....eeeeee.....................hhhhhhhh.hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhh....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
                 1w3h B   1 GLASLADFPIGVAVAASGGNADIFTSSARQNIVRAEFNQITAENIMKMSYMYSGSNFSFTNSDRLVSWAAQNGQTVHGHTLVWHPSYQLPNWASDSNANFRQDFARHIDTVAAHFAGQVKSWDVVNEALFDSADDPDGRGSANGYRQSVFYRQFGGPEYIDEAFRRARAADPTAELYYNDFNTEENGAKTTALVNLVQRLLNNGVPIDGVGFQMHVMNDYPSIANIRQAMQKIVALSPTLKIKITELDVRLNNPYDGNSSNNYTNRNDCAVSCAGLDRQKARYKEIVQAYLEVVPPGRRGGITVWGIADPDSWLYTHQNLPDWPLLFNDNLQPKPAYQGVVEALSGR 347
                                    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(

)

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	d1w3ha_	A:
1b	d1w3hb_	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. Strain: gm83 de3. (2)

1a	1w3hA00	A:-1-346
1b	1w3hB00	B:1-347

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_10-1w3hB01	B:1-344
1b	Glyco_hydro_10-1w3hB02	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 - Thr A:80	[ RasMol ]
		His B:79 - Thr B:80	[ RasMol ]
		Tyr A:220 - Pro A:221	[ RasMol ]
		Tyr B:220 - Pro B:221	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	1w3h
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
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Access by UniProt ID/Accession number
	XYNA_CELJU \| P14768
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	3.2.1.8
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	XYNA_CELJU \| P14768
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UniProtKB/Swiss-Prot
	XYNA_CELJU \| P14768	:	1clx 1e5n 1e8r 1qld 1w2p 1w2v 1w32 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
1w32	THE 3-DIMENSIONAL STRUCTURE OF A THERMOSTABLE MUTANT OF A XYLANASE (XYN10A) FROM CELLVIBRIO JAPONICUS
1xys	CATALYTIC CORE OF XYLANASE A E246C MUTANT

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

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