2XII - JenaLib

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Title :   CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH AN EXTENDED 9-FLUORENONE IMINOSUGAR INHIBITOR

Authors :   A. Lammerts Van Bueren, S. D. Popat, C. H. Lin, G. J. Davies

Date :   30 Jun 10 (Deposition) - 21 Jul 10 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Hydrolase, Fucose (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Lammerts Van Bueren, S. D. Popat, C. H. Lin, G. J. Davies
Structural And Thermodynamic Analyses Of Alpha-L-Fucosidase Inhibitors.
Chembiochem V. 11 1971 2010
PubMed-ID: 20665773 | Reference-DOI: 10.1002/CBIC.201000339

Molecule 1 - ALPHA-L-FUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.51
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	CATALYTIC DOMAIN, 32-484
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818
	Synonym	:	FUCOSIDASE, GLYCOSIDE HYDROLASE, ALPHA-L-FUCOSIDE FUCOHYDROLASE

		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 (4, 9)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	4	Ligand/Ion	SULFATE ION
3	TA9	2	Ligand/Ion	9-OXO-N-[[(2R,3R,4R,5R,6S)-3,4,5-TRIHYDROXY-6-METHYL-PIPERIDIN-2-YL]METHYL]FLUORENE-1-CARBOXAMIDE
4	TYR	2	Mod. Amino Acid	TYROSINE

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	SO4	3	Ligand/Ion	SULFATE ION
3	TA9	1	Ligand/Ion	9-OXO-N-[[(2R,3R,4R,5R,6S)-3,4,5-TRIHYDROXY-6-METHYL-PIPERIDIN-2-YL]METHYL]FLUORENE-1-CARBOXAMIDE
4	TYR	1	Mod. Amino Acid	TYROSINE

Biological Unit 2 (4, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION
3	TA9	1	Ligand/Ion	9-OXO-N-[[(2R,3R,4R,5R,6S)-3,4,5-TRIHYDROXY-6-METHYL-PIPERIDIN-2-YL]METHYL]FLUORENE-1-CARBOXAMIDE
4	TYR	1	Mod. Amino Acid	TYROSINE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:66 , GLU A:87 , TRP A:88 , HIS A:135 , HIS A:136 , TYR A:178 , ASP A:229 , TRP A:232 , ARG A:262 , HIS A:272 , GLU A:288 , TRP A:316	BINDING SITE FOR RESIDUE TA9 A1002
2	AC2	SOFTWARE	HIS B:66 , GLU B:87 , TRP B:88 , HIS B:135 , HIS B:136 , TYR B:178 , ASP B:229 , TRP B:232 , ARG B:262 , HIS B:272 , GLU B:288 , TRP B:316	BINDING SITE FOR RESIDUE TA9 B1002
3	AC3	SOFTWARE	ALA A:387 , ARG A:399 , ASP A:403 , VAL A:405 , HOH A:2339	BINDING SITE FOR RESIDUE TYR A1001
4	AC4	SOFTWARE	ALA B:387 , ARG B:399 , ASP B:403 , VAL B:405 , ALA B:471	BINDING SITE FOR RESIDUE TYR B1001
5	AC5	SOFTWARE	LYS A:237 , ARG A:271 , HOH A:2340 , HOH A:2341 , HOH A:2342 , LYS B:268	BINDING SITE FOR RESIDUE SO4 A1003
6	AC6	SOFTWARE	TYR A:82 , GLY A:83 , HOH A:2343	BINDING SITE FOR RESIDUE SO4 A1004
7	AC7	SOFTWARE	LYS A:372 , ARG A:376 , LYS A:456 , LYS A:457 , ASN A:458	BINDING SITE FOR RESIDUE SO4 A1005
8	AC8	SOFTWARE	LYS A:268 , LYS B:237 , ARG B:271 , HOH B:2166	BINDING SITE FOR RESIDUE SO4 B1003
9	AC9	SOFTWARE	ALA B:85 , GLU B:87 , TRP B:88 , ASN B:314 , TRP B:316 , HOH B:2353	BINDING SITE FOR RESIDUE GOL B1004

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

(no "Cis Peptide Bond" information available for 2XII)

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

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

(no "Exon" information available for 2XII)

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
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Chain A from PDB  Type:PROTEIN  Length:439
 aligned with Q8A3I4_BACTN | Q8A3I4 from UniProtKB/TrEMBL  Length:484

    Alignment length:445
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
        Q8A3I4_BACTN     35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAKGTKSIY  479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee...............hhhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh................................hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.eee...eeeee.....eeeeeee........eeeee..eeeee.........eeeeeeee..------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xii A   35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAA------Y 1001
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       | -    |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                               472   1001

Chain B from PDB  Type:PROTEIN  Length:440
 aligned with Q8A3I4_BACTN | Q8A3I4 from UniProtKB/TrEMBL  Length:484

    Alignment length:445
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474     
        Q8A3I4_BACTN     35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAKGTKSIY  479
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Alpha_L_fucos-2xiiB01 B:35-383                                                                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) Alpha_L_fucos-2xiiB02 B:35-383                                                                                                                                                                                                                                                                                                                               ------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ...............hhhhhhhhhhheeeee..hhhhh...ee..ee...hhhhhhhhh..hhhhhhhhhhhh.....hhhhhhhhhhhhh..eeeeeee...............hhhhh....hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhh...ee.hhhh................................hhhhhhh.eeeee...........hhhhh...hhhhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.............eeeee.....eeeee.eee...eeeee....eeeeeeee.....ee.eeeee..eeeee.........eeeeeeeee..-----. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2xii B   35 EIPLKYGATNEGKRQDPAMQKFRDNRLGAFIHWGLYAIPGGEWNGKVYGGAAEWLKSWAKVPADEWLKLMDQWNPTKFDAKKWAKMAKEMGTKYVKITTKHHEGFCLWPSKYTKYTVANTPYKRDILGELVKAYNDEGIDVHFYFSVMDWSNPDYRYDIKSKEDSIAFSRFLEFTDNQLKELATRYPTVKDFWFDGTWDASVKKNGWWTAHAEQMLKELVPGVAINSRLRADDKGKRHFDSNGRLMGDYESGYERRLPDPVKDLKVTQWDWEACMTIPENQWGYHKDWSLSYVKTPIEVIDRIVHAVSMGGNMVVNFGPQADGDFRPEEKAMATAIGKWMNRYGKAVYACDYAGFEKQDWGYYTRGKNDEVYMVVFNQPYSERLIVKTPKGITVEKATLLTTGEDITVVETTRNEYNVSVPKKNPGEPYVIQLKVRAAK-----Y 1001
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464        |-    |
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                473  1001

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 '\|'

(no "SCOP Domain" information available for 2XII)

(no "CATH Domain" information available for 2XII)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyco_hydro_tim (488)

Family: Alpha_L_fucos (18)

Bacteroides thetaiotaomicron (6)

1a	Alpha_L_fucos-2xiiB01	B:35-383
1b	Alpha_L_fucos-2xiiB02	B:35-383

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8A3I4_BACTN | Q8A3I4)

molecular function
	GO:0004560	alpha-L-fucosidase activity	Catalysis of the reaction: an alpha-L-fucoside + H2O = an alcohol + L-fucose.
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:0006004	fucose metabolic process	The chemical reactions and pathways involving fucose, or 6-deoxygalactose, which has two enantiomers, D-fucose and L-fucose.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xii)

Biological Units
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	2xii
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2wvs	CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 TRAPPED COVALENT INTERMEDIATE FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH 2 -FLUORO-FUCOSYL FLUORIDE USING AN E288Q MUTANT
2wvt	CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH A NOVEL IMINOSUGAR FUCOSIDASE INHIBITOR
2wvu	CRYSTAL STRUCTURE OF A MICHAELIS COMPLEX OF ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON WITH THE SYNTHETIC SUBSTRATE 4-NITROPHENYL-ALPHA-L-FUCOSE
2wvv	CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON
2xib	CRYSTAL STRUCTURE OF AN ALPHA-L-FUCOSIDASE GH29 FROM BACTEROIDES THETAIOTAOMICRON IN COMPLEX WITH DEOXYFUCONOJIRIMYCIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (3, 3)

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