1H4H - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   OLIGOSACCHARIDE-BINDING TO FAMILY 11 XYLANASES: BOTH COVALENT INTERMEDIATE AND MUTANT-PRODUCT COMPLEXES DISPLAY 2,5B CONFORMATIONS AT THE ACTIVE-CENTRE

Authors :   E. Sabini, K. S. Wilson, S. Danielsen, M. Schulein, G. J. Davies

Date :   11 May 01 (Deposition) - 09 May 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Glycoside Hydrolase, Xylanase, Oligosaccharide, Transition-State, Intermediate, Mutant, Boat Conformation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Sabini, G. Sulzenbacher, M. Dauter, Z. Dauter, P. L. Jorgensen, M. Schulein, C. Dupont, G. J. Davies, K. S. Wilson
Catalysis And Specificity In Enzymatic Glycoside Hydrolysis: A 2, 5B Conformation For The Glycosyl- Enzyme Intermediate Revealed By The Structure Of The Bacillus Agaradhaerens Family 11 Xylanase.
Chem. Biol. V. 6 483 1999
PubMed-ID: 10381409 | Reference-DOI: 10.1016/S1074-5521(99)80066-0

Molecule 1 - XYLANASE
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.8
	Engineered	:	YES
	Expression System	:	BACILLUS LICHENIFORMIS
	Expression System Taxid	:	1402
	Fragment	:	FAMILY 11 XYLANASE CATALYTIC DOMAIN
	Mutation	:	YES
	Organism Scientific	:	BACILLUS AGARADHAERENS
	Organism Taxid	:	76935
	Other Details	:	XYLOTRIOSE IN THE ACTIVE SITE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	PCA	4	Mod. Amino Acid	PYROGLUTAMIC ACID
2	XYP	8	Ligand/Ion	BETA-D-XYLOPYRANOSE
3	XYS	4	Ligand/Ion	XYLOPYRANOSE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
3	XYS	1	Ligand/Ion	XYLOPYRANOSE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
3	XYS	1	Ligand/Ion	XYLOPYRANOSE

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
3	XYS	1	Ligand/Ion	XYLOPYRANOSE

Biological Unit 4 (3, 4)

No.	Name	Count	Type	Full Name
1	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID
2	XYP	2	Ligand/Ion	BETA-D-XYLOPYRANOSE
3	XYS	1	Ligand/Ion	XYLOPYRANOSE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:17 , TRP A:19 , ARG A:49 , TYR A:85 , PRO A:133 , SER A:134 , XYP A:1209 , XYS A:1210	BINDING SITE FOR RESIDUE XYP A1208
02	AC2	SOFTWARE	ILE A:8 , TRP A:19 , ILE A:135 , TYR A:177 , XYP A:1208 , HOH A:2129 , HOH A:2131	BINDING SITE FOR RESIDUE XYP A1209
03	AC3	SOFTWARE	TRP A:19 , ASN A:45 , LEU A:47 , TYR A:85 , TYR A:96 , ARG A:129 , PRO A:133 , PHE A:141 , GLN A:143 , XYP A:1208	BINDING SITE FOR RESIDUE XYS A1210
04	AC4	SOFTWARE	GLU B:17 , TRP B:19 , ARG B:49 , TYR B:85 , PRO B:133 , SER B:134 , XYP B:1211 , XYS B:1212	BINDING SITE FOR RESIDUE XYP B1210
05	AC5	SOFTWARE	ILE B:8 , ILE B:135 , XYP B:1210 , HOH B:2116 , HOH B:2142	BINDING SITE FOR RESIDUE XYP B1211
06	AC6	SOFTWARE	TRP B:19 , ASN B:45 , LEU B:47 , TYR B:85 , TRP B:87 , TYR B:96 , ARG B:129 , PRO B:133 , PHE B:141 , GLN B:143 , XYP B:1210	BINDING SITE FOR RESIDUE XYS B1212
07	AC7	SOFTWARE	GLU C:17 , TRP C:19 , ARG C:49 , TYR C:85 , PRO C:133 , SER C:134 , XYP C:1209 , XYS C:1210 , HOH C:2089	BINDING SITE FOR RESIDUE XYP C1208
08	AC8	SOFTWARE	ILE C:135 , XYP C:1208 , HOH C:2089 , HOH C:2105	BINDING SITE FOR RESIDUE XYP C1209
09	AC9	SOFTWARE	ASN C:45 , LEU C:47 , TYR C:85 , TRP C:87 , ALA C:94 , TYR C:96 , ARG C:129 , PRO C:133 , GLN C:143 , XYP C:1208	BINDING SITE FOR RESIDUE XYS C1210
10	BC1	SOFTWARE	GLU D:17 , TRP D:19 , ARG D:49 , TYR D:85 , PRO D:133 , SER D:134 , XYP D:1210 , XYS D:1211 , HOH D:2096	BINDING SITE FOR RESIDUE XYP D1209
11	BC2	SOFTWARE	ILE D:8 , ILE D:135 , XYP D:1209	BINDING SITE FOR RESIDUE XYP D1210
12	BC3	SOFTWARE	ASN D:45 , LEU D:47 , TYR D:85 , TRP D:87 , TYR D:96 , ARG D:129 , PRO D:133 , PHE D:141 , GLN D:143 , XYP D:1209	BINDING SITE FOR RESIDUE XYS D1211

(no "SS Bond" information available for 1H4H)

Asymmetric Unit

No.	Residues
1	Asp A:90	-	Pro A:91
2	Pro A:106	-	Pro A:107
3	Asp B:90	-	Pro B:91
4	Pro B:106	-	Pro B:107
5	Asp C:90	-	Pro C:91
6	Pro C:106	-	Pro C:107
7	Asp D:90	-	Pro D:91
8	Pro D:106	-	Pro D:107

(no "SAP(SNP)/Variant" information available for 1H4H)

(no "PROSITE Motif" information available for 1H4H)

(no "Exon" information available for 1H4H)

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:207
 aligned with Q7SIE2_BACAG | Q7SIE2 from UniProtKB/TrEMBL  Length:209

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q7SIE2_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
               SCOP domains d1h4ha_ A: Xylanase II                                                                                                                                                                                          SCOP domains
               CATH domains -1h4hA00 A:2-207  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeee...eeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h4h A   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
                            |                                                                                                                                                                                                              
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:209
 aligned with Q7SIE2_BACAG | Q7SIE2 from UniProtKB/TrEMBL  Length:209

    Alignment length:209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
         Q7SIE2_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLSTI 209
               SCOP domains d1h4hb_ B: Xylanase II                                                                                                                                                                                            SCOP domains
               CATH domains -1h4hB00 B:2-209  [code=2.60.120.180, no name defined]                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeee...eeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeeee..ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h4h B   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLSTI 209
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200         
                            1-PCA

Chain C from PDB  Type:PROTEIN  Length:207
 aligned with Q7SIE2_BACAG | Q7SIE2 from UniProtKB/TrEMBL  Length:209

    Alignment length:207
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
         Q7SIE2_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
               SCOP domains d1h4hc_ C: Xylanase II                                                                                                                                                                                          SCOP domains
               CATH domains -1h4hC00 C:2-207  [code=2.60.120.180, no name defined]                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeee..eeeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeeee..ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h4h C   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS 207
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
                            1-PCA

Chain D from PDB  Type:PROTEIN  Length:208
 aligned with Q7SIE2_BACAG | Q7SIE2 from UniProtKB/TrEMBL  Length:209

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
         Q7SIE2_BACAG     1 QIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLST 208
               SCOP domains d1h4hd_ D: Xylanase II                                                                                                                                                                                           SCOP domains
               CATH domains -1h4hD00 D:2-208  [code=2.60.120.180, no name defined]                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee..eeeeeee....eeeeee.....eeeeee...eeeeeeeee.....hhhhhh.eeeeeeeeeee...eeeeeeeeee...eeeeeeeee...........eeeee..eeeeeeeeeeeee......eeeeeeeeee.....eeeehhhhhhhhhhhh.....eeeeeeeeeeee...eeeeeeeeeeee..ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1h4h D   1 xIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNAYLCVYGWTVDPLVAYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLST 208
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
                            1-PCA

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(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: Xylanase/endoglucanase 11/12 (93)

Protein domain: Xylanase II (65)

Bacillus agaradhaerens [TaxId: 76935] (4)

1a	d1h4ha_	A:
1b	d1h4hb_	B:
1c	d1h4hc_	C:
1d	d1h4hd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.180, no name defined] (77)

Bacillus agaradhaerens. Organism_taxid: 76935. (4)

1a	1h4hA00	A:2-207
1b	1h4hC00	C:2-207
1c	1h4hD00	D:2-208
1d	1h4hB00	B:2-209

(no "Pfam Domain" information available for 1H4H)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q7SIE2_BACAG | Q7SIE2)

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.

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		Pro D:106 - Pro D:107	[ RasMol ]

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1h4g	OLIGOSACCHARIDE-BINDING TO FAMILY 11 XYLANASES: BOTH COVALENT INTERMEDIATE AND MUTANT-PRODUCT COMPLEXES DISPLAY 2,5B CONFORMATIONS AT THE ACTIVE-CENTRE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 16)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

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