2F8Q - JenaLib

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Title :   AN ALKALI THERMOSTABLE F/10 XYLANASE FROM ALKALOPHILIC BACILLUS SP. NG-27

Authors :   S. Ramakumar, K. Manikandan, A. Bhardwaj, A. Ghosh, V. S. Reddy

Date :   03 Dec 05 (Deposition) - 26 Sep 06 (Release) - 10 Sep 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Alkali Thermostable Family 10 Xylanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Manikandan, A. Bhardwaj, N. Gupta, N. K. Lokanath, A. Ghosh, V. S. Reddy, S. Ramakumar
Crystal Structures Of Native And Xylosaccharide-Bound Alkal Thermostable Xylanase From An Alkalophilic Bacillus Sp. Ng-27: Structural Insights Into Alkalophilicity And Implications For Adaptation To Polyextreme Conditions.
Protein Sci. V. 15 1951 2006
PubMed-ID: 16823036 | Reference-DOI: 10.1110/PS.062220206
(for further references see the PDB file header)

Molecule 1 - ALKALINE THERMOSTABLE ENDOXYLANASE
	Chains	:	A, B
	EC Number	:	3.2.1.8
	Organism Scientific	:	BACILLUS SP. NG-27
	Organism Taxid	:	65673

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:292 , ARG A:351 , ASP A:354 , HOH A:810 , HOH A:841 , HOH A:990 , HOH A:1053	BINDING SITE FOR RESIDUE MG A 801
2	AC2	SOFTWARE	ASN B:292 , ARG B:351 , ASP B:354 , HOH B:1019 , HOH B:1042 , HOH B:1045 , HOH B:1064	BINDING SITE FOR RESIDUE MG B 802

(no "SS Bond" information available for 2F8Q)

Asymmetric Unit

No.	Residues
1	His A:85	-	Thr A:86
2	Thr A:202	-	Pro A:203
3	Trp A:235	-	Pro A:236
4	Trp A:267	-	Pro A:268
5	Arg A:270	-	Pro A:271
6	His B:85	-	Thr B:86
7	Thr B:202	-	Pro B:203
8	Trp B:235	-	Pro B:236
9	Trp B:267	-	Pro B:268
10	Arg B:270	-	Pro B:271

(no "SAP(SNP)/Variant" information available for 2F8Q)

(no "PROSITE Motif" information available for 2F8Q)

(no "Exon" information available for 2F8Q)

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:353
 aligned with O30700_9BACI | O30700 from UniProtKB/TrEMBL  Length:405

    Alignment length:353
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   
         O30700_9BACI    53 QPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 405
               SCOP domains d2f8qa_ A: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2f8qA00 A:2-354 Glycosidases                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeee.........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhhh..eeeeeeeee.................hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh.................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f8q A   2 QPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

Chain B from PDB  Type:PROTEIN  Length:353
 aligned with O30700_9BACI | O30700 from UniProtKB/TrEMBL  Length:405

    Alignment length:353
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   
         O30700_9BACI    53 QPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 405
               SCOP domains d2f8qb_ B: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2f8qB00 B:2-354 Glycosidases                                                                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.hhhhhh....eeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhh.......hhhhhhhhhhhhhh..eeee.........hhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee...............hhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhh.....eeee..ee.....hhhhhhhhhhhhhh...eeeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh..................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2f8q B   2 QPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

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: automated matches (49)

Bacillus sp. [TaxId: 65673] (2)

1a	d2f8qa_	A:
1b	d2f8qb_	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)

Ng-27 (Bacillus sp) (2)

1a	2f8qA00	A:2-354
1b	2f8qB00	B:2-354

(no "Pfam Domain" information available for 2F8Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B (O30700_9BACI | O30700)

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.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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
		Arg A:270 - Pro A:271	[ RasMol ]
		Arg B:270 - Pro B:271	[ RasMol ]
		His A:85 - Thr A:86	[ RasMol ]
		His B:85 - Thr B:86	[ RasMol ]
		Thr A:202 - Pro A:203	[ RasMol ]
		Thr B:202 - Pro B:203	[ RasMol ]
		Trp A:235 - Pro A:236	[ RasMol ]
		Trp A:267 - Pro A:268	[ RasMol ]
		Trp B:235 - Pro B:236	[ RasMol ]
		Trp B:267 - Pro B:268	[ RasMol ]

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