2CER - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH PHENETHYL-SUBSTITUTED GLUCOIMIDAZOLE

Authors :   T. M. Gloster, S. Roberts, M. Moracci, A. Vasella, G. J. Davies

Date :   10 Feb 06 (Deposition) - 27 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

Keywords :   Glycoside Hydrolase, Inhibitor, Transition State Mimic, Family 1, Glucoimidazole, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Gloster, S. Roberts, G. Perugino, M. Rossi, M. Moracci, N. Panday, M. Terinek, A. Vasella, G. J. Davies
Structural, Kinetic, And Thermodynamic Analysis Of Glucoimidazole-Derived Glycosidase Inhibitors.
Biochemistry V. 45 11879 2006
PubMed-ID: 17002288 | Reference-DOI: 10.1021/BI060973X

Molecule 1 - BETA-GLUCOSIDASE A
	Chains	:	A, B
	EC Number	:	3.2.1.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	GENTIOBIASE, CELLOBIASE, BETA-D-GLUCOSIDE GLUCOHYDROLASE

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	PGI	2	Ligand/Ion	(5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	PGI	1	Ligand/Ion	(5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	PGI	1	Ligand/Ion	(5R,6R,7S,8S)-5-(HYDROXYMETHYL)-2-(2-PHENYLETHYL)-1,5,6,7,8,8A-HEXAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:455 , ARG A:463 , GLU A:464 , GLU A:474	BINDING SITE FOR RESIDUE ACT A1491
2	AC2	SOFTWARE	TYR A:2 , HIS A:410 , ARG A:411 , ASN A:414	BINDING SITE FOR RESIDUE ACT A1492
3	AC3	SOFTWARE	THR B:373 , ASN B:377 , SER B:415	BINDING SITE FOR RESIDUE ACT B1491
4	AC4	SOFTWARE	GLN A:18 , HIS A:150 , TRP A:151 , ASN A:205 , GLU A:206 , SER A:265 , TYR A:322 , TRP A:361 , GLU A:387 , TRP A:425 , GLU A:432 , TRP A:433 , PHE A:441 , HOH A:2332	BINDING SITE FOR RESIDUE PGI A1490
5	AC5	SOFTWARE	GLN B:18 , HIS B:150 , TRP B:151 , ASN B:205 , GLU B:206 , ALA B:263 , ASN B:264 , TYR B:322 , TRP B:361 , GLU B:387 , TRP B:425 , GLU B:432 , TRP B:433 , PHE B:441 , HOH B:2315	BINDING SITE FOR RESIDUE PGI B1490

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

Asymmetric Unit

No.	Residues
1	Pro A:223	-	Pro A:224
2	Trp A:425	-	Ser A:426
3	Pro B:223	-	Pro B:224
4	Trp B:425	-	Ser B:426

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGAL_SULSO	8-22	2	A:8-22 B:8-22
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGAL_SULSO	383-391	2	A:383-391 B:383-391

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGAL_SULSO	8-22	1	A:8-22 -
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGAL_SULSO	383-391	1	A:383-391 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	BGAL_SULSO	8-22	1	- B:8-22
2	GLYCOSYL_HYDROL_F1_1	PS00572	Glycosyl hydrolases family 1 active site.	BGAL_SULSO	383-391	1	- B:383-391

(no "Exon" information available for 2CER)

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:489
 aligned with BGAL_SULSO | P22498 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:489
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480         
           BGAL_SULSO     1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
               SCOP domains d2cera_ A: beta-Glycosidase                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cerA00 A:1-489 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh......................hhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhheeee..eeee.........eeeeeeeeeeeeee...................................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh...eeeeee........hhh.hhh....eee......eeehhhhhhhhhhhhhheehhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GLYCOSYL_HYDROL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cer A   1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480

Chain B from PDB  Type:PROTEIN  Length:489
 aligned with BGAL_SULSO | P22498 from UniProtKB/Swiss-Prot  Length:489

    Alignment length:489
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480         
           BGAL_SULSO     1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
               SCOP domains d2cerb_ B: beta-Glycosidase                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cerB00 B:1-489 Glycosidases                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeeee.hhhhhh..........hhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhh...eeeee.hhhhhh......................hhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeeeee.........hhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhheee....eee..........eeeeeeeeeeeeee..................................hhhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhhhhhhh...eeeeee........hhh.hhh....eee......eeehhhhhhhhhhhhhheehhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------GLYCOSYL_HYDROL------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GLYCOSYL_-------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cer B   1 MYSFPNSFRFGWSQAGFQSEMGTPGSEDPNTDWYKWVHDPENMAAGLVSGDLPENGPGYWGNYKTFHDNAQKMGLKIARLNVEWSRIFPNPLPRPQNFDESKQDVTEVEINENELKRLDEYANKDALNHYREIFKDLKSRGLYFILNMYHWPLPLWLHDPIRVRRGDFTGPSGWLSTRTVYEFARFSAYIAWKFDDLVDEYSTMNEPNVVGGLGYVGVKSGFPPGYLSFELSRRAMYNIIQAHARAYDGIKSVSKKPVGIIYANSSFQPLTDKDMEAVEMAENDNRWWFFDAIIRGEITRGNEKIVRDDLKGRLDWIGVNYYTRTVVKRTEKGYVSLGGYGHGCERNSVSLAGLPTSDFGWEFFPEGLYDVLTKYWNRYHLYMYVTENGIADDADYQRPYYLVSHVYQVHRAINSGADVRGYLHWSLADNYEWASGFSMRFGLLKVDYNTKRLYWRPSALVYREIATNGAITDEIEHLNSVPPVKPLRH 489
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480

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: Family 1 of glycosyl hydrolase (102)

Protein domain: beta-Glycosidase (10)

Sulfolobus solfataricus [TaxId: 2287] (9)

1a	d2cera_	A:
1b	d2cerb_	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)

Sulfolobus solfataricus. Organism_taxid: 2287. (9)

1a	2cerA00	A:1-489
1b	2cerB00	B:1-489

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (BGAL_SULSO | P22498)

molecular function
	GO:0004565	beta-galactosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-galactose residues in beta-D-galactosides.
	GO:0008422	beta-glucosidase activity	Catalysis of the hydrolysis of terminal, non-reducing beta-D-glucose residues with release of beta-D-glucose.
	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:1901657	glycosyl compound metabolic process	The chemical reactions and pathways involving glycosyl compound.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:223 - Pro A:224	[ RasMol ]
		Pro B:223 - Pro B:224	[ RasMol ]
		Trp A:425 - Ser A:426	[ RasMol ]
		Trp B:425 - Ser B:426	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2cer
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	3.2.1.21
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	BGAL_SULSO \| P22498
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UniProtKB/Swiss-Prot
	BGAL_SULSO \| P22498	:	1gow 1uwi 1uwq 1uwr 1uws 1uwt 1uwu 2ceq 4eam 4ean 5i3d 5ixe

1gow	BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS
1uwi	CRYSTAL STRUCTURE OF MUTATED BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS, WORKING AT MODERATE TEMPERATURE
1uwq	STRUCTURE OF BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS
1uwr	STRUCTURE OF BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH 2-DEOXY-2- FLUORO-GALACTOSE
1uws	STRUCTURE OF BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH 2-DEOXY-2- FLUORO-GLUCOSE
1uwt	STRUCTURE OF BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH D- GALACTOHYDROXIMO-1,5-LACTAM
1uwu	STRUCTURE OF BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH D- GLUCOHYDROXYIMO-1,5-LACTAM
2ceq	BETA-GLYCOSIDASE FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH GLUCOIMIDAZOLE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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Related Entries

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Related Entries Specified in the PDB File