4ATL - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF RAUCAFFRICINE GLUCOSIDASE IN COMPLEX WITH GLUCOSE

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

Date :   08 May 12 (Deposition) - 30 Jan 13 (Release) - 07 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.52

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

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

Reference :   L. Xia, C. Rajendran, M. Ruppert, S. Panjikar, M. Wang, J. Stoeckigt
High Speed X-Ray Analysis Of Plant Enzymes At Room Temperature
Phytochemistry V. 91 88 2013
PubMed-ID: 22704651 | Reference-DOI: 10.1016/J.PHYTOCHEM.2012.05.009
(for further references see the PDB file header)

Molecule 1 - RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.125
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector	:	PQE-2
	Expression System Vector Type	:	PLASMID
	Organism Common	:	SERPENTWOOD
	Organism Scientific	:	RAUVOLFIA SERPENTINA
	Organism Taxid	:	4060

		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 (1, 2)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:36 , HIS A:140 , ASN A:185 , GLU A:186 , TYR A:347 , GLU A:420 , TRP A:469 , GLU A:476 , TRP A:477 , PHE A:485	BINDING SITE FOR RESIDUE BGC A1513
2	AC2	SOFTWARE	GLN B:36 , HIS B:140 , ASN B:185 , GLU B:186 , TYR B:347 , GLU B:420 , TRP B:469 , GLU B:476 , TRP B:477 , PHE B:485	BINDING SITE FOR RESIDUE BGC B1513

(no "SS Bond" information available for 4ATL)

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 4ATL)

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, 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 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	- B:26-40

(no "Exon" information available for 4ATL)

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
                                    21        31        41        51        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       411       421       431       441       451       461       471       481       491       501       511 
            RG1_RAUSE    12 NDATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGRTSPEHVNHPTVQHRCSTVAPQCICSTGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNASTNSSGSNNFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFH 512
               SCOP domains d4atla_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..............hhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh..........------------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..-------..hhhhhh.........................hhhhhhhhhhhhhhhh...eeeeee..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeeee.......hhhhh.......eee.......eeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4atl A  12 NDATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGR------------------------STGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNAS-------NFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFH 512
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    |    -         -       231       241       251       261       271       281       291       301       311       321       331       341       351    |    -  |    371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
                                                                                                                                                                                                                            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
                                    21        31        41        51        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       411       421       431       441       451       461       471       481       491       501       511 
            RG1_RAUSE    12 NDATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGRTSPEHVNHPTVQHRCSTVAPQCICSTGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNASTNSSGSNNFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFH 512
               SCOP domains d4atlb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh....eeeee.hhhhhh..........hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhh.hhhhhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh..........------------------------......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhh....eeeeeeeeeeeeee..-------..hhhhhh......ee..ee.............hhhhhhhhhhhhhhhh...eeeeee..........hhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeeeee......hhhhhhhh....eee.......eeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------GLYCOSYL_HYDROL---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4atl B  12 NDATRISRSDFPADFIMGTGSSAYQIEGGARDGGRGPSIWDTFTHRRPDMIRGGTNGDVAVDSYHLYKEDVNILKNLGLDAYRFSISWSRVLPGGRLSGGVNKEGINYYNNLIDGLLANGIKPFVTLFHWDVPQALEDEYGGFLSPRIVDDFCEYAELCFWEFGDRVKHWMTLNEPWTFSVHGYATGLYAPGRGR------------------------STGNPGTEPYWVTHHLLLAHAAAVELYKNKFQRGQEGQIGISHATQWMEPWDENSASDVEAAARALDFMLGWFMEPITSGDYPKSMKKFVGSRLPKFSPEQSKMLKGSYDFVGLNYYTASYVTNAS-------NFSYNTDIHVTYETDRNGVPIGPQSGSDWLLIYPEGIRKILVYTKKTYNVPLIYVTENGVDDVKNTNLTLSEARKDSMRLKYLQDHIFNVRQAMNDGVNVKGYFAWSLLDNFEWGEGYGVRFGIIHIDYNDNFARYPKDSAVWLMNSFH 512
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    |    -         -       231       241       251       261       271       281       291       301       311       321       331       341       351    |    -  |    371       381       391       401       411       421       431       441       451       461       471       481       491       501       511 
                                                                                                                                                                                                                            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	d4atla_	A:
1b	d4atlb_	B:

(no "CATH Domain" information available for 4ATL)

(no "Pfam Domain" information available for 4ATL)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	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 ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4atl
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	RG1_RAUSE \| Q9SPP9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.2.1.125
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RG1_RAUSE \| Q9SPP9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	RG1_RAUSE \| Q9SPP9	:	3u57 3u5u 3u5y 3zj6 4a3y 4atd 4ek7

4a3y	CRYSTAL STRUCTURE OF RAUCAFFRICINE GLUCOSIDASE FROM AJMALINE BIOSYNTHESIS PATHWAY
4atd	CRYSTAL STRUCTURE OF NATIVE RAUCAFFRICINE GLUCOSIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File