2FGL - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

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

Date :   22 Dec 05 (Deposition) - 26 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   F/10 Family Alkali-Thermostable 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 Alkali 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
	Fragment	:	RESIDUES 52 - 405
	Organism Scientific	:	BACILLUS SP. NG-27
	Organism Taxid	:	65673
	Strain	:	BACILLUS SP. NG-27

		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, 13)

No.	Name	Count	Type	Full Name
1	LXC	1	Ligand/Ion	BETA-L-XYLOPYRANOSE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	XYS	8	Ligand/Ion	XYLOPYRANOSE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	LXC	-1	Ligand/Ion	BETA-L-XYLOPYRANOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	XYS	5	Ligand/Ion	XYLOPYRANOSE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	LXC	1	Ligand/Ion	BETA-L-XYLOPYRANOSE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	XYS	3	Ligand/Ion	XYLOPYRANOSE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:52 , HIS A:85 , ASN A:148 , GLU A:149 , GLN A:228 , HIS A:230 , GLU A:259 , TRP A:311 , TRP A:319 , XYS A:701 , HOH A:803	BINDING SITE FOR RESIDUE XYS A 700
02	AC2	SOFTWARE	GLU A:48 , ASN A:49 , LYS A:52 , GLN A:92 , TRP A:311 , XYS A:700 , XYS A:702 , HOH A:810	BINDING SITE FOR RESIDUE XYS A 701
03	AC3	SOFTWARE	GLU A:26 , GLU A:48 , ASN A:49 , HIS A:317 , XYS A:701 , HOH A:908	BINDING SITE FOR RESIDUE XYS A 702
04	AC4	SOFTWARE	TYR A:197 , ARG A:323 , XYS A:704 , HOH A:804 , HOH A:809 , GLU B:158	BINDING SITE FOR RESIDUE XYS A 703
05	AC5	SOFTWARE	ASN A:198 , GLN A:232 , TRP A:235 , TRP A:267 , XYS A:703 , HOH A:867	BINDING SITE FOR RESIDUE XYS A 704
06	AC6	SOFTWARE	LYS B:52 , HIS B:85 , ASN B:148 , GLU B:149 , GLN B:228 , HIS B:230 , GLU B:259 , TRP B:311 , TRP B:319 , XYS B:706 , HOH B:842	BINDING SITE FOR RESIDUE XYS B 705
07	AC7	SOFTWARE	GLU B:48 , ASN B:49 , LYS B:52 , GLN B:92 , TRP B:311 , XYS B:705 , XYS B:707 , HOH B:835	BINDING SITE FOR RESIDUE XYS B 706
08	AC8	SOFTWARE	GLU B:26 , GLU B:48 , ASN B:49 , HIS B:317 , XYS B:706 , HOH B:856	BINDING SITE FOR RESIDUE XYS B 707
09	AC9	SOFTWARE	ASN B:198 , ARG B:323 , HOH B:934 , HOH B:935	BINDING SITE FOR RESIDUE LXC B 708
10	BC1	SOFTWARE	ASN A:292 , ARG A:351 , ASP A:354	BINDING SITE FOR RESIDUE MG A 601
11	BC2	SOFTWARE	SER A:18 , ASP A:302 , LEU A:305 , HOH A:884	BINDING SITE FOR RESIDUE MG A 602
12	BC3	SOFTWARE	ASN B:292 , ARG B:351 , ASP B:354 , HOH B:845	BINDING SITE FOR RESIDUE MG B 603
13	BC4	SOFTWARE	SER B:18 , ASP B:302 , LEU B:305	BINDING SITE FOR RESIDUE MG B 604

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

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 2FGL)

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

(no "Exon" information available for 2FGL)

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:354
 aligned with O30700_9BACI | O30700 from UniProtKB/TrEMBL  Length:405

    Alignment length:354
                                    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       361       371       381       391       401    
         O30700_9BACI    52 VQPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 405
               SCOP domains d2fgla_ A: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fglA00 A:1-354 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.................hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh.................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fgl A   1 VQPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    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       350

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with O30700_9BACI | O30700 from UniProtKB/TrEMBL  Length:405

    Alignment length:354
                                    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       361       371       381       391       401    
         O30700_9BACI    52 VQPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 405
               SCOP domains d2fglb_ B: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2fglB00 B:1-354 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.................hhhhhhhhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhh.................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2fgl B   1 VQPFAWQVASLADRYEESFDIGAAVEPHQLNGRQGKVLKHHYNSIVAENAMKPISLQPEEGVFTWDGADAIVEFARKNNMNLRFHTLVWHNQVPDWFFLDEEGNPMVEETNEAKRQANKELLLERLETHIKTVVERYKDDVTAWDVVNEVVDDGTPNERGLRESVWYQITGDEYIRVAFETARKYAGEDAKLFINDYNTEVTPKRDHLYNLVQDLLADGVPIDGVGHQAHIQIDWPTIDEIRTSMEMFAGLGLDNQVTELDVSLYGWPPRPAFPTYDAIPQERFQAQADRYNQLFELYEELDADLSSVTFWGIADNHTWLDDRAREYNDGVGKDAPFVFDPNYRVKPAFWRIID 354
                                    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       350

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	d2fgla_	A:
1b	d2fglb_	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	2fglA00	A:1-354
1b	2fglB00	B:1-354

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

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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	Ligands, Modified Residues, Ions
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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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	2fgl
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	O30700_9BACI \| O30700	:	2f8q 4qce 4qcf 4qdm 5eb8 5eba 5efd 5eff

2f8q	NATIVE STRUCTURE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

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