1N23 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   (+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG, PYROPHOSPHATE, AND (1R,4S)-2-AZABORNANE

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 :   2.40

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 (3, 10)

No.	Name	Count	Type	Full Name
1	2BN	2	Ligand/Ion	(1R,4S)-2-AZABORNANE
2	MG	6	Ligand/Ion	MAGNESIUM ION
3	POP	2	Ligand/Ion	PYROPHOSPHATE 2-

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:351 , ASP A:355 , MG A:702 , POP A:901 , HOH A:964 , HOH A:965	BINDING SITE FOR RESIDUE MG A 701
02	AC2	SOFTWARE	ASP A:351 , ASP A:355 , MG A:701 , POP A:901 , HOH A:960 , HOH A:962 , HOH A:963	BINDING SITE FOR RESIDUE MG A 702
03	AC3	SOFTWARE	ASP A:496 , THR A:500 , GLU A:504 , POP A:901 , HOH A:961	BINDING SITE FOR RESIDUE MG A 703
04	AC4	SOFTWARE	ASP B:351 , ASP B:355 , MG B:705 , POP B:902 , HOH B:967 , HOH B:968 , HOH B:969	BINDING SITE FOR RESIDUE MG B 704
05	AC5	SOFTWARE	ASP B:351 , ASP B:355 , MG B:704 , POP B:902 , HOH B:971 , HOH B:972	BINDING SITE FOR RESIDUE MG B 705
06	AC6	SOFTWARE	ASP B:496 , THR B:500 , GLU B:504 , POP B:902 , HOH B:970	BINDING SITE FOR RESIDUE MG B 706
07	AC7	SOFTWARE	THR A:348 , VAL A:452 , ALA A:453 , TYR A:572 , PHE A:578 , POP A:901 , HOH A:959	BINDING SITE FOR RESIDUE 2BN A 801
08	AC8	SOFTWARE	THR B:348 , VAL B:452 , ALA B:453 , TYR B:572 , PHE B:578 , POP B:902 , HOH B:904	BINDING SITE FOR RESIDUE 2BN B 802
09	AC9	SOFTWARE	ARG A:314 , ASP A:351 , ASP A:355 , ARG A:493 , ASP A:496 , THR A:500 , GLU A:504 , LYS A:512 , MG A:701 , MG A:702 , MG A:703 , 2BN A:801 , HOH A:959 , HOH A:960 , HOH A:961 , HOH A:963 , HOH A:964 , HOH A:965 , HOH A:966 , HOH A:972	BINDING SITE FOR RESIDUE POP A 901
10	BC1	SOFTWARE	ARG B:314 , ASP B:351 , ASP B:355 , ARG B:493 , ASP B:496 , THR B:500 , GLU B:504 , LYS B:512 , MG B:704 , MG B:705 , MG B:706 , 2BN B:802 , HOH B:904 , HOH B:966 , HOH B:967 , HOH B:969 , HOH B:970 , HOH B:971 , HOH B:972 , HOH B:1002	BINDING SITE FOR RESIDUE POP B 902

(no "SS Bond" information available for 1N23)

(no "Cis Peptide Bond" information available for 1N23)

(no "SAP(SNP)/Variant" information available for 1N23)

(no "PROSITE Motif" information available for 1N23)

(no "Exon" information available for 1N23)

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:533
 aligned with BPPS_SALOF | O81192 from UniProtKB/Swiss-Prot  Length:598

    Alignment length:544
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594    
           BPPS_SALOF    55 RRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
               SCOP domains d1n23a1 A:55-270 (+)-bornyl diphosphate synthase                                                                                                                                                                        d1n23a2 A:271-598 (+)-bornyl diphosphate synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------1n23A01 A:80-285 Isoprenoid Synthase - domain 1                                                                                                                                                               1n23A02 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....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n23 A  55 RRSGNYQPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCF-------MDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLD----EIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
                                    64        74        84        94       104       114       124       134     |   -   |   154       164       174       184       194       204       214       224  |    234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594    
                                                                                                               140     148                                                                            227  232

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

    Alignment length:538
                                    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       490       500       510       520       530       540       550       560       570       580       590        
           BPPS_SALOF    61 QPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKCFHNNEVEKMDLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDEGGNEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
               SCOP domains d1n23b1 B:61-270 (+)-bornyl diphosphate synthase                                                                                                                                                                  d1n23b2 B:271-598 (+)-bornyl diphosphate synthase                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------1n23B01 B:80-285 Isoprenoid Synthase - domain 1                                                                                                                                                               1n23B02 B:286-598 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                                                           CATH domains
           Pfam domains (1) ----Terpene_synth-1n23B01 B:65-245                                                                                                                                                       -----------------------------Terpene_synth_C-1n23B03 B:275-544                                                                                                                                                                                                                                             ------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) ----Terpene_synth-1n23B02 B:65-245                                                                                                                                                       -----------------------------Terpene_synth_C-1n23B04 B:275-544                                                                                                                                                                                                                                             ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .....hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...---------hhhhhhhhhhhhhhh....hhhhhhhhh.........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...--...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh............hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n23 B  61 QPALWDSNYIQSLNTPYTEERHLDRKAELIVQVRILLKEKMEPVQQLELIHDLKYLGLSDFFQDEIKEILGVIYNEHKC---------DLYFTALGFRLLRQHGFNISQDVFNCFKNEKGIDFKASLAQDTKGMLQLYEASFLLRKGEDTLELAREFATKCLQKKLDE--NEIDENLLLWIRHSLDLPLHWRIQSVEARWFIDAYARRPDMNPLIFELAKLNFNIIQATHQQELKDLSRWWSRLCFPEKLPFVRDRLVESFFWAVGMFEPHQHGYQRKMAATIIVLATVIDDIYDVYGTLDELELFTDTFKRWDTESITRLPYYMQLCYWGVHNYISDAAYDILKEHGFFCLQYLRKSVVDLVEAYFHEAKWYHSGYTPSLDEYLNIAKISVASPAIISPTYFTFANASHDTAVIDSLYQYHDILCLAGIILRLPDDLGTSYFELARGDVPKTIQCYMKETNASEEEAVEHVKFLIREAWKDMNTAIAAGYPFPDGMVAGAANIGRVAQFIYLHGDGFGVQHSKTYEHIAGLLFEPYA 598
                                    70        80        90       100       110       120       130        |-       150       160       170       180       190       200       210       220       | -|      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       490       500       510       520       530       540       550       560       570       580       590        
                                                                                                        139       149                                                                            228  |                                                                                                                                                                                                                                                                                                                                                                               
                                                                                                                                                                                                    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	1n23A01	A:80-285
1b	1n23B01	B:80-285

Architecture: Orthogonal Bundle (10391)

Topology: Farnesyl Diphosphate Synthase (109)

Homologous Superfamily: Farnesyl Diphosphate Synthase (109)

Garden sage (Salvia officinalis) (7)

2a	1n23A02	A:286-598
2b	1n23B02	B:286-598

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

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
1n24	(+)-BORNYL DIPHOSPHATE SYNTHASE: COMPLEX WITH MG AND PRODUCT

Description

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Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

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SCOP Domains (2, 4)

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