1N24 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND PRODUCT

Authors :   D. A. Whittington, M. L. Wise, M. Urbansky, R. M. Coates, R. B. Croteau, D. W. Christianson

Date :   21 Oct 02 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

Keywords :   Terpene Synthase Fold, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. A. Whittington, M. L. Wise, M. Urbansky, R. M. Coates, R. B. Croteau, D. W. Christianson
Bornyl Diphosphate Synthase: Structure And Strategy For Carbocation Manipulation By A Terpenoid Cyclase
Proc. Natl. Acad. Sci. Usa V. 99 15375 2002
PubMed-ID: 12432096 | Reference-DOI: 10.1073/PNAS.232591099
(for further references see the PDB file header)

Molecule 1 - (+)-BORNYL DIPHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	5.5.1.8
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSBET
	Expression System Strain	:	BLR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUE 50-598
	Organism Common	:	GARDEN SAGE
	Organism Scientific	:	SALVIA OFFICINALIS
	Organism Taxid	:	38868

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	BP2	2	Ligand/Ion	(+)-BORNYL DIPHOSPHATE
2	MG	6	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:351 , ASP A:355 , MG A:703 , BP2 A:801 , HOH A:883 , HOH A:884 , HOH A:885	BINDING SITE FOR RESIDUE MG A 701
2	AC2	SOFTWARE	ASP A:496 , THR A:500 , GLU A:504 , BP2 A:801 , HOH A:880	BINDING SITE FOR RESIDUE MG A 702
3	AC3	SOFTWARE	ASP A:351 , ASP A:355 , MG A:701 , BP2 A:801 , HOH A:881 , HOH A:882	BINDING SITE FOR RESIDUE MG A 703
4	AC4	SOFTWARE	ASP B:351 , ASP B:355 , MG B:705 , BP2 B:802 , HOH B:864 , HOH B:865 , HOH B:866	BINDING SITE FOR RESIDUE MG B 704
5	AC5	SOFTWARE	ASP B:351 , ASP B:355 , MG B:704 , BP2 B:802 , HOH B:862 , HOH B:863	BINDING SITE FOR RESIDUE MG B 705
6	AC6	SOFTWARE	ASP B:496 , THR B:500 , BP2 B:802 , HOH B:861	BINDING SITE FOR RESIDUE MG B 706
7	AC7	SOFTWARE	ARG A:314 , THR A:348 , ASP A:351 , ASP A:355 , VAL A:452 , ARG A:493 , ASP A:496 , THR A:500 , GLU A:504 , LYS A:512 , TYR A:572 , PHE A:578 , MG A:701 , MG A:702 , MG A:703 , HOH A:879 , HOH A:880 , HOH A:881 , HOH A:883 , HOH A:891	BINDING SITE FOR RESIDUE BP2 A 801
8	AC8	SOFTWARE	ARG B:314 , THR B:348 , ASP B:351 , ASP B:355 , VAL B:452 , ARG B:493 , ASP B:496 , THR B:500 , LYS B:512 , TYR B:572 , PHE B:578 , MG B:704 , MG B:705 , MG B:706 , HOH B:861 , HOH B:862 , HOH B:863 , HOH B:864 , HOH B:865	BINDING SITE FOR RESIDUE BP2 B 802

(no "SS Bond" information available for 1N24)

(no "Cis Peptide Bond" information available for 1N24)

(no "SAP(SNP)/Variant" information available for 1N24)

(no "PROSITE Motif" information available for 1N24)

(no "Exon" information available for 1N24)

Asymmetric/Biological 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:534
 aligned with BPPS_SALOF | O81192 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:545
                                    63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593     
           BPPS_SALOF    54 IRRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
               SCOP domains d1n24a1 A:54-270 (+)-bornyl diphosphate synthase                                                                                                                                                                         d1n24a2 A:271-598 (+)-bornyl diphosphate synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------1n24A01 A:80-285 Isoprenoid Synthase - domain 1                                                                                                                                                               1n24A02 A:286-598 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....-------hhhhhhhhhhhhhhh....hhhhhhhhh.......hhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..----..hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n24 A  54 IRRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFH-------DLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLD----EIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
                                    63        73        83        93       103       113       123       133       | -     | 153       163       173       183       193       203       213       223   |   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593     
                                                                                                                 141     149                                                                           227  232

Chain B from PDB  Type:PROTEIN  Length:527
 aligned with BPPS_SALOF | O81192 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:537
                                    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       521       531       541       551       561       571       581       591       
           BPPS_SALOF    62 PALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
               SCOP domains d1n24b1 B:62-270 (+)-bornyl diphosphate synthase                                                                                                                                                                 d1n24b2 B:271-598 (+)-bornyl diphosphate synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------1n24B01 B:80-285 Isoprenoid Synthase - domain 1                                                                                                                                                               1n24B02 B:286-598 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh............hhhhhhhhhhhhhhh....hhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.--...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh----.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh......----hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n24 B  62 PALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDE--NEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGT----LARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGF----SKTYEHIAGLLFEPYA 598
                                    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        |-   |   511       521       531       541       551       561       571      |  - |     591       
                                                                                                                                                                                                228  |                                                                                                                                                                                                                                                                          500  505                                                                      578  583               
                                                                                                                                                                                                   231

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Alpha/alpha barrel (251)

Topology: Isoprenoid Synthase; domain 1 (16)

Homologous Superfamily: Isoprenoid Synthase - domain 1 (16)

Garden sage (Salvia officinalis) (7)

1a	1n24A01	A:80-285
1b	1n24B01	B:80-285

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Garden sage (Salvia officinalis) (7)

2a	1n24A02	A:286-598
2b	1n24B02	B:286-598

(no "Pfam Domain" information available for 1N24)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (BPPS_SALOF | O81192)

molecular function
	GO:0047926	geranyl-diphosphate cyclase activity	Catalysis of the reaction: geranyl diphosphate = (2S)-bornyl diphosphate.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0010333	terpene synthase activity	Catalysis of the formation of cyclic terpenes through the cyclization of linear terpenes (e.g. isopentenyl-PP, geranyl-PP, farnesyl-PP and geranylgeranyl-PP) containing varying numbers of isoprene units.
biological process
	GO:0046211	(+)-camphor biosynthetic process	The chemical reactions and pathways resulting in the formation of (+)-camphor, a bicyclic monoterpene ketone.
	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.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n24)

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	1n24
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	5.5.1.8
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UniProtKB/Swiss-Prot
	BPPS_SALOF \| O81192	:	1n1b 1n1z 1n20 1n21 1n22 1n23

1n1b	(+)-BORNYL DIPHOSPHATE SYNTHASE
1n1z	(+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND PYROPHOSPHATE
1n20	(+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND 3-AZA- 2,3-DIHYDROGERANYL DIPHOSPHATE
1n21	(+)-BORNYL DIPHOSPHATE SYNTHASE: COCRYSTAL WITH MG AND 3- AZA-2,3-DIHYDROGERANYL DIPHOSPHATE
1n22	(+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (4R)-7-AZA-7,8-DIHYDROLIMONENE
1n23	(+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (1R,4S)-2-AZABORNANE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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