3U5U - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURES OF ALKALOID BIOSYNTHETIC GLUCOSIDASES DECODE SUBSTRATE SPECIFICITY

Authors :   L. Xia, M. Ruppert, M. Wang, S. Panjikar, H. Lin, C. Rajendran, L. Barleb J. Stoeckigt

Date :   11 Oct 11 (Deposition) - 30 Nov 11 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Raucaffricine Glucosidase (Rg), Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Xia, M. Ruppert, M. Wang, S. Panjikar, H. Lin, C. Rajendran, L. Barleben, J. Stockigt
Structures Of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity.
Acs Chem. Biol. V. 7 226 2012
PubMed-ID: 22004291 | Reference-DOI: 10.1021/CB200267W

Molecule 1 - RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.125
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 1-513
	Mutation	:	YES
	Organism Common	:	DEVILPEPPER
	Organism Scientific	:	RAUVOLFIA SERPENTINA
	Organism Taxid	:	4060

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:107 , THR B:432 , SER B:434	BINDING SITE FOR RESIDUE CL B 514
2	AC2	SOFTWARE	THR A:432 , SER A:434 , ARG B:107 , SER B:109	BINDING SITE FOR RESIDUE CL B 515

(no "SS Bond" information available for 3U5U)

Asymmetric Unit

No.	Residues
1	Ala A:201	-	Pro A:202
2	Trp A:469	-	Ser A:470
3	Ala B:201	-	Pro B:202
4	Trp B:469	-	Ser B:470

(no "SAP(SNP)/Variant" information available for 3U5U)

Asymmetric Unit (1, 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.	RG1_RAUSE	26-40	2	A:26-40 B:26-40

Biological Unit 1 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	RG1_RAUSE	26-40	8	A:26-40 B:26-40

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	RG1_RAUSE	26-40	1	A:26-40 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GLYCOSYL_HYDROL_F1_2	PS00653	Glycosyl hydrolases family 1 N-terminal signature.	RG1_RAUSE	26-40	1	- B:26-40

(no "Exon" information available for 3U5U)

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:470
 aligned with RG1_RAUSE | Q9SPP9 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:501
                                    22        32        42        52        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       412       422       432       442       452       462       472       482       492       502       512 
            RG1_RAUSE    13 DATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGRTSPEHVNHPTVQHRCSTVAPQCICSTGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNASTNSSGSNNFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFHK 513
               SCOP domains d3u5ua_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh..........------------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee....hhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..-------..hhhhhh.eeee....................hhhhhhhhhhhhhhhh...eeeee...........hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhh.......eee.......eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GLYCOSYL_HYDROL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u5u A  13 DATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNQPWTFSVHGYATGLYAPGRGR------------------------STGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNAS-------NFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFHK 513
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   |     -         -       232       242       252       262       272       282       292       302       312       322       332       342       352   |     - |     372       382       392       402       412       422       432       442       452       462       472       482       492       502       512 
                                                                                                                                                                                                                           206                      231                                                                                                                          356     364

Chain B from PDB  Type:PROTEIN  Length:470
 aligned with RG1_RAUSE | Q9SPP9 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:501
                                    22        32        42        52        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       412       422       432       442       452       462       472       482       492       502       512 
            RG1_RAUSE    13 DATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGRTSPEHVNHPTVQHRCSTVAPQCICSTGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNASTNSSGSNNFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFHK 513
               SCOP domains d3u5ub_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhh..........------------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee......hhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..-------..hhhhhh.eeee.ee..ee.............hhhhhhhhhhhhhhh....eeeee...........hhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeeeee......hhhhh.......eee.......eeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GLYCOSYL_HYDROL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u5u B  13 DATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNQPWTFSVHGYATGLYAPGRGR------------------------STGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNAS-------NFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFHK 513
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   |     -         -       232       242       252       262       272       282       292       302       312       322       332       342       352   |     - |     372       382       392       402       412       422       432       442       452       462       472       482       492       502       512 
                                                                                                                                                                                                                           206                      231                                                                                                                          356     364

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: automated matches (180)

Protein domain: automated matches (180)

Rauvolfia serpentina [TaxId: 4060] (12)

1a	d3u5ua_	A:
1b	d3u5ub_	B:

(no "CATH Domain" information available for 3U5U)

(no "Pfam Domain" information available for 3U5U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RG1_RAUSE | Q9SPP9)

molecular function
	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:0050247	raucaffricine beta-glucosidase activity	Catalysis of the reaction: H(2)O + raucaffricine = D-glucose + vomilenine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0050506	vomilenine glucosyltransferase activity	Catalysis of the reaction: UDP-D-glucose + vomilenine = H(+) + raucaffricine + UDP.
biological process
	GO:0009821	alkaloid biosynthetic process	The chemical reactions and pathways resulting in the formation of alkaloids, nitrogen-containing natural products which are not otherwise classified as nonprotein amino acids, amines, peptides, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones, or primary metabolite (such as purine or pyrimidine bases).
	GO:0009820	alkaloid metabolic process	The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:201 - Pro A:202	[ RasMol ]
		Ala B:201 - Pro B:202	[ RasMol ]
		Trp A:469 - Ser A:470	[ RasMol ]
		Trp B:469 - Ser B:470	[ RasMol ]

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	3.2.1.125
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	RG1_RAUSE \| Q9SPP9	:	3u57 3u5y 3zj6 4a3y 4atd 4atl 4ek7

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Ligands, Modified Residues, Ions (1, 2)

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