3BNY - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE COMPLEXED WITH 2-FLUOROFARNESYL DIPHOSPHATE (2F-FPP)

Authors :   E. Y. Shishova, D. W. Christianson

Date :   14 Dec 07 (Deposition) - 25 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

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

Keywords :   Sesquiterpene Cyclase, Isoprenoid, Farnesyl Diphosphate, Magnesium, Cyclization, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Y. Shishova, F. Yu, D. J. Miller, J. A. Faraldos, Y. Zhao, R. M. Coates, R. K. Allemann, D. E. Cane, D. W. Christianson
X-Ray Crystallographic Studies Of Substrate Binding To Aristolochene Synthase Suggest A Metal Ion Binding Sequence For Catalysis
J. Biol. Chem. V. 283 15431 2008
PubMed-ID: 18385128 | Reference-DOI: 10.1074/JBC.M800659200
(for further references see the PDB file header)

Molecule 1 - ARISTOLOCHENE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.3.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11-RASA
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	ARI1
	Organism Scientific	:	ASPERGILLUS TERREUS
	Organism Taxid	:	33178

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	BME	3	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	1	Ligand/Ion	CHLORIDE ION
3	FPF	4	Ligand/Ion	(2Z,6E)-2-FLUORO-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL TRIHYDROGEN DIPHOSPHATE
4	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	BME	1	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FPF	2	Ligand/Ion	(2Z,6E)-2-FLUORO-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL TRIHYDROGEN DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	FPF	2	Ligand/Ion	(2Z,6E)-2-FLUORO-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL TRIHYDROGEN DIPHOSPHATE
4	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN D:219 , SER D:223 , GLU D:227 , HOH D:1278	BINDING SITE FOR RESIDUE MG D 701
2	AC2	SOFTWARE	ARG B:314 , HOH B:1366	BINDING SITE FOR RESIDUE CL B 500
3	AC3	SOFTWARE	CYS C:25 , ARG C:62 , CYS C:65 , LEU C:66 , PRO D:27 , HOH D:1298	BINDING SITE FOR RESIDUE BME C 1270
4	AC4	SOFTWARE	CYS B:25 , ARG B:62	BINDING SITE FOR RESIDUE BME B 1271
5	AC5	SOFTWARE	GLU C:30 , HOH C:1280 , CYS D:25 , ARG D:62 , CYS D:65	BINDING SITE FOR RESIDUE BME D 1272
6	AC6	SOFTWARE	TYR A:67 , PHE A:153 , LYS A:181 , ASN A:219 , ASN A:305 , TRP A:308 , TYR A:315	BINDING SITE FOR RESIDUE FPF A 400
7	AC7	SOFTWARE	TYR B:67 , PHE B:87 , ASP B:90 , PHE B:153 , LYS B:181 , LEU B:184 , ASN B:219 , TRP B:308 , ARG B:314 , TYR B:315 , HOH B:1281	BINDING SITE FOR RESIDUE FPF B 401
8	AC8	SOFTWARE	TYR C:67 , LEU C:86 , PHE C:87 , PHE C:153 , LEU C:184 , ASN C:219 , TRP C:308 , ARG C:314 , TYR C:315 , HOH C:1386	BINDING SITE FOR RESIDUE FPF C 402
9	AC9	SOFTWARE	TYR D:67 , LEU D:86 , PHE D:87 , PHE D:153 , LYS D:181 , LEU D:184 , ASN D:219 , SER D:223 , LYS D:226 , GLU D:227 , ARG D:314 , TYR D:315 , HOH D:1287	BINDING SITE FOR RESIDUE FPF D 403

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

(no "Cis Peptide Bond" information available for 3BNY)

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

(no "PROSITE Motif" information available for 3BNY)

(no "Exon" information available for 3BNY)

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:294
 aligned with ARIS_ASPTE | Q9UR08 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:305
                                    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     
           ARIS_ASPTE    13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSKTAHSEGGILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
               SCOP domains d3bnya_ A: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bnyA00 A:13-317 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-----------..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bny A  13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELY-----------LCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222      |  -       242       252       262       272       282       292       302       312     
                                                                                                                                                                                                                                                  229         241

Chain B from PDB  Type:PROTEIN  Length:296
 aligned with ARIS_ASPTE | Q9UR08 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:305
                                    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     
           ARIS_ASPTE    13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSKTAHSEGGILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
               SCOP domains d3bnyb_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bnyB00 B:13-317 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---------...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bny B  13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYT---------ILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       | -       242       252       262       272       282       292       302       312     
                                                                                                                                                                                                                                                   230       240

Chain C from PDB  Type:PROTEIN  Length:293
 aligned with ARIS_ASPTE | Q9UR08 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:305
                                    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     
           ARIS_ASPTE    13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSKTAHSEGGILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
               SCOP domains d3bnyc_ C: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bnyC00 C:13-317 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..----------..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bny C  13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYT----------LCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEG--TPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       | -       242       252       262       272       282  |  | 292       302       312     
                                                                                                                                                                                                                                                   230        241                                         285  |                             
                                                                                                                                                                                                                                                                                                             288

Chain D from PDB  Type:PROTEIN  Length:297
 aligned with ARIS_ASPTE | Q9UR08 from UniProtKB/Swiss-Prot  Length:320

    Alignment length:305
                                    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     
           ARIS_ASPTE    13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSKTAHSEGGILCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
               SCOP domains d3bnyd_ D: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3bnyD00 D:13-317 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bny D  13 SLEPPPSTFQPLCHPLVEEVSKEVDGYFLQHWNFPNEKARKKFVAAGFSRVTCLYFPKALDDRIHFACRLLTVLFLIDDLLEYMSFEEGSAYNEKLIPISRGDVLPDRSIPVEYIIYDLWESMRAHDREMADEILEPVFLFMRAQTDRTRARPMGLGGYLEYRERDVGKELLAALMRFSMGLKLSPSELQRVREIDANCSKHLSVVNDIYSYEKELYTSK--------LCTSVQILAQEADVTAEAAKRVLFVMCREWELRHQLLVARLSAEGLETPGLAAYVEGLEYQMSGNELWSQTTLRYSV 317
                                    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     
                                                                                                                                                                                                                                                     232      241

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: All alpha proteins (14657)

Fold: Terpenoid synthases (196)

Superfamily: Terpenoid synthases (196)

Family: Aristolochene/pentalenene synthase (16)

Protein domain: automated matches (11)

Aspergillus terreus [TaxId: 33178] (11)

1a	d3bnya_	A:
1b	d3bnyb_	B:
1c	d3bnyc_	C:
1d	d3bnyd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Aspergillus terreus. Organism_taxid: 33178. (5)

1a	3bnyD00	D:13-317
1b	3bnyB00	B:13-317
1c	3bnyA00	A:13-317
1d	3bnyC00	C:13-317

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ARIS_ASPTE | Q9UR08)


GO:0045483	aristolochene synthase activity	Catalysis of the reaction: trans,trans-farnesyl diphosphate = aristolochene + diphosphate.
GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3bny)

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2e4o	X-RAY CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE FROM ASPERGILLUS TERREUS
2oa6	ARISTOLOCHENE SYNTHASE FROM ASPERGILLUS TERREUS COMPLEXED WITH PYROPHOSPHATE AND 3 MG2+ IONS
3bnx	CRYSTAL STRUCTURE OF ARISTOLOCHENE SYNTHASE COMPLEXED WITH FARNESYL DIPHOSPHATE

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)

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SCOP Domains (1, 4)

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