3KRP - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   MINT HETEROTETRAMERIC GERANYL PYROPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM AND GPP

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

Date :   19 Nov 09 (Deposition) - 23 Feb 10 (Release) - 12 Feb 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.42

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, Isoprene Biosynthesis, Isoprenyl Pyrophosphate Synthase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. -H. Chang, F. -L. Hsieh, T. -P. Ko, K. -H. Teng, P. -H. Liang, A. H. -J. Wang
Structure Of A Heterotetrameric Geranyl Pyrophosphate Synthase From Mint (Mentha Piperita) Reveals Intersubunit Regulation
Plant Cell V. 22 454 2010
PubMed-ID: 20139160 | Reference-DOI: 10.1105/TPC.109.071738

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
	Gene	:	GPPS LARGE SUBUNIT
	Organism Common	:	PEPPERMINT
	Organism Scientific	:	MENTHA X PIPERITA
	Organism Taxid	:	34256
	Synonym	:	GPPS LARGE SUBUNIT, 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
	Gene	:	GPPS SMALL SUBUNIT
	Organism Common	:	PEPPERMINT
	Organism Scientific	:	MENTHA X PIPERITA
	Organism Taxid	:	34256
	Synonym	:	GPPS SMALL SUBUNIT, 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 (4, 7)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	PPV	1	Ligand/Ion	PYROPHOSPHATE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PPV	1	Ligand/Ion	PYROPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	GPP	-1	Ligand/Ion	GERANYL DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PPV	1	Ligand/Ion	PYROPHOSPHATE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	PPV	-1	Ligand/Ion	PYROPHOSPHATE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:83 , ASP A:89 , ARG A:94 , LYS A:180 , HOH A:732 , HOH A:733 , MG A:905 , MG A:906	BINDING SITE FOR RESIDUE PPV A 901
2	AC2	SOFTWARE	ASP A:83 , ASP A:84 , ASP A:89 , ASP A:91 , HOH A:732 , PPV A:901 , MG A:906	BINDING SITE FOR RESIDUE MG A 905
3	AC3	SOFTWARE	ASP A:83 , ASP A:89 , HOH A:733 , PPV A:901 , MG A:905	BINDING SITE FOR RESIDUE MG A 906
4	AC4	SOFTWARE	PHE A:2 , ALA C:41 , THR C:42 , SER C:45 , THR C:46 , HIS C:70	BINDING SITE FOR RESIDUE EDO C 902
5	AC5	SOFTWARE	LYS D:44 , ARG D:47 , HIS D:76 , LEU D:80 , ASP D:83 , ARG D:95 , GLN D:156 , LYS D:180 , PHE D:217 , GLN D:218 , HOH D:317	BINDING SITE FOR RESIDUE GPP D 900
6	AC6	SOFTWARE	ASP D:83 , ASP D:89 , ASP D:91 , HOH D:296 , HOH D:570	BINDING SITE FOR RESIDUE MG D 903
7	AC7	SOFTWARE	ASP D:84 , ASP D:91 , LEU D:93 , ARG D:94 , HOH D:570	BINDING SITE FOR RESIDUE MG D 904

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

Asymmetric Unit

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

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

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

(no "Exon" information available for 3KRP)

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 d3krpa_ 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..hhhhhhhhhhhhhhhhhhhhhhhhhhh...----------------..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krp 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:256
 aligned with Q9SBR4_MENPI | Q9SBR4 from UniProtKB/TrEMBL  Length:313

    Alignment length:259
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297         
         Q9SBR4_MENPI    48 SQPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 306
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh...---.hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krp B   1 MQPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELG---GKNAELMSSLVA 259
                                    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         
                                                                                                                                                                                                                                                                             244 248

Chain C from PDB  Type:PROTEIN  Length:259
 aligned with Q9SBR4_MENPI | Q9SBR4 from UniProtKB/TrEMBL  Length:313

    Alignment length:259
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297         
         Q9SBR4_MENPI    48 SQPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 306
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------polyprenyl_synt-3krpC01 C:28-214                                                                                                                                                           --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------polyprenyl_synt-3krpC02 C:28-214                                                                                                                                                           --------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krp C   1 MQPYWAAIEADIERYLKKSITIRPPETVFGPMHHLTFAAPATAASTLCLAACELVGGDRSQAMAAAAAIHLVHAAAYVHEHLPLTDGSRPVSKPAIQHKYGPNVELLTGDGIVPFGFELLAGSVDPARTDDPDRILRVIIEISRAGGPEGMISGLHREEEIVDGNTSLDFIEYVCKKKYGEMHACGAACGAILGGAAEEEIQKLRNFGLYQGTLRGMMEMKNSHQLIDENIIGKLKELALEELGGFHGKNAELMSSLVA 259
                                    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

Chain D from PDB  Type:PROTEIN  Length:284
 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 d3krpd_ D: automated matches                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------polyprenyl_synt-3krpD01 D:31-290                                                                                                                                                                                                                                    ----- Pfam domains (1)
           Pfam domains (2) ------------------------------polyprenyl_synt-3krpD02 D:31-290                                                                                                                                                                                                                                    ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.-----------hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3krp D   1 MFDFDGYMLRKAKSVNKALEAAVQMKEPLKIHESMRYSLLAGGKRVRPMLCIAACELVGGDESTAMPAACAVEMIHTMSLMHDDLPCMDNDDLRRGKPTNHMAFGESVAVLAGDALLSFAFEHVAAATKGAPPERIVRVLGELAVSIGSEGLVAGQVVDVCSEGMAEVGLDHLEFIHHHKTAALLQGSVVLGAILGGGKEEEVAKLRKFANCIGLLFQVVDDILDVTKSSKELGK-----------TYPKLIGVEKSKEFADRLNREAQEQLLHFHPHRAAPLIALANYIAYRDN 295
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |    -      |250       260       270       280       290     
                                                                                                                                                                                                                                                                    235         247

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	d3krpa_	A:
1b	d3krpd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: polyprenyl_synt (86)

Mentha piperita (Peppermint) (6)

1a	polyprenyl_synt-3krpD01	D:31-290
1b	polyprenyl_synt-3krpD02	D:31-290
1c	polyprenyl_synt-3krpC01	C:28-214
1d	polyprenyl_synt-3krpC02	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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	Cis Peptide Bonds
		Glu A:27 - Pro A:28	[ RasMol ]
		Glu D:27 - Pro D:28	[ RasMol ]
		Pro B:24 - Pro B:25	[ RasMol ]
		Pro C:24 - Pro C:25	[ RasMol ]

Biological Units
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Access by PDB/NDB ID
	3krp
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	2.5.1.1
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

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