3OAC - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   MINT DELETION MUTANT OF HETEROTETRAMERIC GERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH LIGANDS

Authors :   F. -L. Hsieh, T. -H. Chang, T. -P. Ko, A. H. -J. Wang

Date :   05 Aug 10 (Deposition) - 03 Nov 10 (Release) - 26 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Prenyltransferase, All Alpha-Helices Fold, Prenyltransferase And Monoterpene Biosynthesis, Chroloplast, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. -L. Hsieh, T. -H. Chang, T. -P. Ko, A. H. -J. Wang
Enhanced Specificity Of Mint Geranyl Pyrophosphate Synthase By Modifying The R-Loop Interactions
J. Mol. Biol. V. 404 859 2010
PubMed-ID: 20965200 | Reference-DOI: 10.1016/J.JMB.2010.10.011

Molecule 1 - GERANYL DIPHOSPHATE SYNTHASE LARGE SUBUNIT
	Chains	:	A, D
	EC Number	:	2.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 84-377
	Organism Common	:	PEPPERMINT
	Organism Scientific	:	MENTHA X PIPERITA
	Organism Taxid	:	34256
	Synonym	:	GERANYL PYROPHOSPHATE SYNTHASE LARGE SUBUNIT, GPP SYNTHASE LARGE SUBUNIT

Molecule 2 - GERANYL DIPHOSPHATE SYNTHASE SMALL SUBUNIT
	Chains	:	B, C
	EC Number	:	2.5.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET37
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 49-313
	Mutation	:	YES
	Organism Common	:	PEPPERMINT
	Organism Scientific	:	MENTHA X PIPERITA
	Organism Taxid	:	34256
	Synonym	:	GPP SYNTHASE SMALL SUBUNIT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	DST	1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	DST	1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	DST	-1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	IPE	-1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	DST	1	Ligand/Ion	DIMETHYLALLYL S-THIOLODIPHOSPHATE
2	IPE	1	Ligand/Ion	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY D:43 , LYS D:44 , ARG D:47 , HIS D:76 , ARG D:95 , THR D:181 , GLN D:218 , ASP D:221 , HOH D:296 , HOH D:300 , HOH D:318 , DST D:2002	BINDING SITE FOR RESIDUE IPE D 2001
2	AC2	SOFTWARE	SER D:79 , ASP D:83 , ASP D:89 , ARG D:94 , LEU D:152 , GLN D:156 , LYS D:180 , LYS D:235 , HOH D:297 , IPE D:2001 , MG D:3001 , MG D:3002	BINDING SITE FOR RESIDUE DST D 2002
3	AC3	SOFTWARE	ASP D:83 , ASP D:89 , LYS D:245 , DST D:2002	BINDING SITE FOR RESIDUE MG D 3001
4	AC4	SOFTWARE	ASP D:83 , ASP D:89 , ASP D:91 , LYS D:239 , DST D:2002	BINDING SITE FOR RESIDUE MG D 3002

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

Asymmetric Unit

No.	Residues
1	Glu A:27	-	Pro A:28
2	Pro B:24	-	Pro B:25
3	Leu B:82	-	Pro B:83
4	Pro C:24	-	Pro C:25
5	Glu D:27	-	Pro D:28

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

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

(no "Exon" information available for 3OAC)

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:279
 aligned with Q9SBR3_MENPI | Q9SBR3 from UniProtKB/TrEMBL  Length:377

    Alignment length:295
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
         Q9SBR3_MENPI    83 AFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTKSSKELGKTAGKDLVADKTTYPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 377
               SCOP domains d3oaca_ A: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh----------------..hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oac A   1 MFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTK----------------KTTYPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       | -         -    |  250       260       270       280       290     
                                                                                                                                                                                                                                                             228              245

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with Q9SBR4_MENPI | Q9SBR4 from UniProtKB/TrEMBL  Length:313

    Alignment length:258
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298        
         Q9SBR4_MENPI    49 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 306
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..----------.......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oac B   2 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLP----------PAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 259
                                    11        21        31        41        51        61        71        81 |       -  |    101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        
                                                                                                            83         94

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with Q9SBR4_MENPI | Q9SBR4 from UniProtKB/TrEMBL  Length:313

    Alignment length:258
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298        
         Q9SBR4_MENPI    49 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 306
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------------polyprenyl_synt-3oacC01 C:28-214                                                                                                                                                           --------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------polyprenyl_synt-3oacC02 C:28-214                                                                                                                                                           --------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..----------.......hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh....hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3oac C   2 QPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLP----------PAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 259
                                    11        21        31        41        51        61        71        81 |       -  |    101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251        
                                                                                                            83         94

Chain D from PDB  Type:PROTEIN  Length:295
 aligned with Q9SBR3_MENPI | Q9SBR3 from UniProtKB/TrEMBL  Length:377

    Alignment length:295
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
         Q9SBR3_MENPI    83 AFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTKSSKELGKTAGKDLVADKTTYPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 377
               SCOP domains d3oacd_ D: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------polyprenyl_synt-3oacD01 D:31-290                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) ------------------------------polyprenyl_synt-3oacD02 D:31-290                                                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh........ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oac D   1 MFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTKSSKELGKTAGKDLVADKTTYPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290

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: automated matches (68)

Protein domain: automated matches (68)

Mentha x [TaxId: 34256] (7)

1a	d3oaca_	A:
1b	d3oacd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: polyprenyl_synt] (86)

Family: polyprenyl_synt (86)

Mentha piperita (Peppermint) (6)

1a	polyprenyl_synt-3oacD01	D:31-290
1b	polyprenyl_synt-3oacD02	D:31-290
1c	polyprenyl_synt-3oacC01	C:28-214
1d	polyprenyl_synt-3oacC02	C:28-214

Asymmetric Unit(hide GO term definitions)

Chain A,D (Q9SBR3_MENPI | Q9SBR3)

molecular function
	GO:0004161	dimethylallyltranstransferase activity	Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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.
biological process
	GO:0033384	geranyl diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of geranyl diphosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

Chain B,C (Q9SBR4_MENPI | Q9SBR4)

biological process
	GO:0008299		isoprenoid biosynthetic process		The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		IPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Glu A:27 - Pro A:28	[ RasMol ]
		Glu D:27 - Pro D:28	[ RasMol ]
		Leu B:82 - Pro B:83	[ RasMol ]
		Pro B:24 - Pro B:25	[ RasMol ]
		Pro C:24 - Pro C:25	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]
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Access by PDB/NDB ID
	3oac
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	Q9SBR4_MENPI \| Q9SBR4
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3kra	WILD-TYPE PROTEIN IN COMPLEX WITH MG IONS
3krc	WILD-TYPE PROTEIN IN COMPLEX WITH IPP
3krf	WILD-TYPE PROTEIN IN COMPLEX WITH MG IONS, IPP, AND DMASPP
3kro	WILD-TYPE PROTEIN IN COMPLEX WITH MG IONS, IPP, AND DMASPP
3krp	WILD-TYPE PROTEIN IN COMPLEX WITH MG IONS AND GPP
3oab

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (5, 6)

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Related Entries Specified in the PDB File