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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF FAMILY 10 XYLANASE FROM BACILLUS HALODURANS

Authors :   G. Mamo, M. Thunnissen, R. Hatti-Kaul, B. Mattiasson

Date :   21 Mar 07 (Deposition) - 27 May 08 (Release) - 18 Jan 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Xylan Degradation, Xylanase Structure, Glycosidase, Alkaliphilic, Endoxylanase, Bacillus Halodurans, Alkaline Adaptation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Mamo, M. Thunnissen, R. Hatti-Kaul, B. Mattiasson
An Alkaline Active Xylanase: Insights Into Mechanisms Of High Ph Catalytic Adaptation
Biochimie V. 91 1187 2009
PubMed-ID: 19567261 | Reference-DOI: 10.1016/J.BIOCHI.2009.06.017

Molecule 1 - ALKALINE ACTIVE ENDOXYLANASE
	Chains	:	A
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22 BPLUS
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 47-396
	Organism Scientific	:	BACILLUS HALODURANS
	Organism Taxid	:	86665
	Other Details	:	ADDITIONAL HIS-TAG PRESENT IN THIS ENTRY. I359D360H361H362H363H364H365H366
	Strain	:	S7
	Synonym	:	ENDOXYLANASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CU	1	Ligand/Ion	COPPER (II) ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:298 , GLU A:302 , HIS A:362 , HIS A:366	BINDING SITE FOR RESIDUE CU A1367
2	AC2	SOFTWARE	ASP A:298 , ARG A:357 , ASP A:360 , HOH A:2169 , HOH A:2204 , HOH A:2206 , HOH A:2208	BINDING SITE FOR RESIDUE CA A1368
3	AC3	SOFTWARE	GLN A:28 , SER A:308 , ILE A:311 , HOH A:2013 , HOH A:2015 , HOH A:2180	BINDING SITE FOR RESIDUE CA A1369
4	AC4	SOFTWARE	ASP A:30 , GLU A:91 , HIS A:365 , HOH A:2077	BINDING SITE FOR RESIDUE CA A1370
5	AC5	SOFTWARE	TYR A:282 , ASP A:321 , ASP A:327 , ASP A:340	BINDING SITE FOR RESIDUE CA A1371

(no "SS Bond" information available for 2UWF)

Asymmetric/Biological Unit

No.	Residues
1	His A:95	-	Thr A:96
2	Trp A:241	-	Pro A:242
3	Trp A:273	-	Pro A:274
4	Thr A:276	-	Gly A:277

(no "SAP(SNP)/Variant" information available for 2UWF)

Asymmetric/Biological Unit (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_BACHD	51-396	1	A:15-360
2	GH10_1	PS00591	Glycosyl hydrolases family 10 (GH10) active site.	XYNA_BACHD	294-304	1	A:258-268

(no "Exon" information available for 2UWF)

Asymmetric/Biological 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:356
 aligned with Q17TM8_BACHO | Q17TM8 from UniProtKB/TrEMBL  Length:396

    Alignment length:356
                                                                                                                                                                                                                                                                                                                                                                                       396      
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
         Q17TM8_BACHO    47 DQPFAWQVASLSERYQEQFDIGAAVEPYQLEGRQAQILKHHYNSLVAENAMKPVSLQPREGEWNWEGADKIVEFARKHNMELRFHTLVWHSQVPEWFFIDENGNRMVDETDPEKRKANKQLLLERMENHIKTVVERYKDDVTSWDVVNEVIDDGGGLRESEWYQITGTDYIKVAFETARKYGGEEAKLYINDYNTEVPSKRDDLYNLVKDLLEQGVPIDGVGHQSHIQIGWPSIEDTRASFEKFTSLGLDNQVTELDMSLYGWPPTGAYTSYDDIPEELFQAQADRYDQLFELYEELSATISSVTFWGIADNHTWLDDRAREYNNGVGVDAPFVFDHNYRVKPAYWRIID------   -
               SCOP domains d2uwfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2uwfA00 A:11-366 Glycosidases                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------Glyco_hydro_10-2uwfA01 A:20-360                                                                                                                                                                                                                                                                                                                      ------ Pfam domains
         Sec.struct. author ....hhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhhh.eeee...ee....hhhhh.......hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh...eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh.................hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwf A  11 NQPFAWQVASLSERYQEQFDIGAAVEPYQLEGRQAQILKHHYNSLVAENAMKPVSLQPREGEWNWEGADKIVEFARKHNMELRFHTLVWHSQVPEWFFIDENGNRMVDETDPEKRKANKQLLLERMENHIKTVVERYKDDVTSWDVVNEVIDDDGGLRESEWYQITGTDYIKVAFETARKYGGEEAKLYINDYNTEVPSKRDDLYNLVKDLLEQGVPIDGVGHQSHIQIGWPSIEDTRASFEKFTSLGLDNQVTELDMSLYGWPPTGAYTSYDDIPEELFQAQADRYDQLFELYEELSATISSVTFWGIADNHTWLDDRAREYNNGVGVDAPFVFDHNYRVKPAYWRIIDHHHHHH 366
                                    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       350       360

Chain A from PDB  Type:PROTEIN  Length:356
 aligned with XYNA_BACHD | P07528 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:356
                                                                                                                                                                                                                                                                                                                                                                                       396      
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396      
           XYNA_BACHD    47 DQPFAWQVASLSERYQEQFDIGAAVEPYQLEGRQAQILKHHYNSLVAENAMKPESLQPREGEWNWEGADKIVEFARKHNMELRFHTLVWHSQVPEWFFIDEDGNRMVDETDPDKREANKQLLLERMENHIKTVVERYKDDVTSWDVVNEVIDDGGGLRESEWYQITGTDYIKVAFETARKYGGEEAKLYINDYNTEVPSKRDDLYNLVKDLLEQGVPIDGVGHQSHIQIGWPSIEDTRASFEKFTSLGLDNQVTELDMSLYGWPPTGAYTSYDDIPAELLQAQADRYDQLFELYEELAADISSVTFWGIADNHTWLDGRAREYNNGVGIDAPFVFDHNYRVKPAYWRIID------   -
               SCOP domains d2uwfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2uwfA00 A:11-366 Glycosidases                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ---------Glyco_hydro_10-2uwfA01 A:20-360                                                                                                                                                                                                                                                                                                                      ------ Pfam domains
         Sec.struct. author ....hhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhhh.eeee...ee....hhhhh.......hhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh.....eeee.........hhhhhhhhhhhhhh...eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhh.................hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----GH10_2  PDB: A:15-360 UniProt: 51-396                                                                                                                                                                                                                                                                                                                     ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GH10_1     -------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwf A  11 NQPFAWQVASLSERYQEQFDIGAAVEPYQLEGRQAQILKHHYNSLVAENAMKPVSLQPREGEWNWEGADKIVEFARKHNMELRFHTLVWHSQVPEWFFIDENGNRMVDETDPEKRKANKQLLLERMENHIKTVVERYKDDVTSWDVVNEVIDDDGGLRESEWYQITGTDYIKVAFETARKYGGEEAKLYINDYNTEVPSKRDDLYNLVKDLLEQGVPIDGVGHQSHIQIGWPSIEDTRASFEKFTSLGLDNQVTELDMSLYGWPPTGAYTSYDDIPEELFQAQADRYDQLFELYEELSATISSVTFWGIADNHTWLDDRAREYNNGVGVDAPFVFDHNYRVKPAYWRIIDHHHHHH 366
                                    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       350       360

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/Biological 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: automated matches (49)

Bacillus halodurans [TaxId: 86665] (1)

d2uwfa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Glycosidases (843)

Bacillus halodurans. Organism_taxid: 86665. Strain: s7. (1)

2uwfA00

A:11-366

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Glyco_hydro_10 (42)

Bacillus halodurans (1)

Glyco_hydro_10-2uwfA01

A:20-360

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q17TM8_BACHO | Q17TM8)

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.

Chain A (XYNA_BACHD | P07528)

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/Biological Unit
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	Cis Peptide Bonds
		His A:95 - Thr A:96	[ RasMol ]
		Thr A:276 - Gly A:277	[ RasMol ]
		Trp A:241 - Pro A:242	[ RasMol ]
		Trp A:273 - Pro A:274	[ RasMol ]

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	XYNA_BACHD \| P07528
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Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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