3APZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   APO FORM OF ARABIDOPSIS MEDIUM/LONG-CHAIN LENGTH PRENYL PYROPHOSPHATE SYNTHASE

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

Date :   24 Oct 10 (Deposition) - 19 Jan 11 (Release) - 29 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Prenyltransferase, All Alpha-Helices Fold, Chroloplast, Transferase, Isoprenoid Biosynthetic Process (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. -L. Hsieh, T. -H. Chang, T. -P. Ko, A. H. -J. Wang
Structure And Mechanism Of An Arabidopsis Medium/Long-Chain-Length Prenyl Pyrophosphate Synthase
Plant Physiol. V. 155 1079 2011
PubMed-ID: 21220764 | Reference-DOI: 10.1104/PP.110.168799

Molecule 1 - GERANYL DIPHOSPHATE SYNTHASE
	Chains	:	A, B
	EC Number	:	2.5.1.30
	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	:	RESIDUES IN UNP 76-422
	Gene	:	ATNPPPS, GPPS
	Organism Common	:	THALE-CRESS
	Organism Scientific	:	ARABIDOPSIS THALIANA
	Organism Taxid	:	3702

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A
Biological Unit 2 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3APZ)

(no "Site" information available for 3APZ)

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

Asymmetric Unit

No.	Residues
1	Val A:33	-	Pro A:34
2	Val B:33	-	Pro B:34

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	SPS3_ARATH	178-192	2	A:104-109 B:104-110
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	SPS3_ARATH	300-312	2	A:226-238 B:226-238

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	SPS3_ARATH	178-192	2	A:104-109 -
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	SPS3_ARATH	300-312	2	A:226-238 -

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	SPS3_ARATH	178-192	2	- B:104-110
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	SPS3_ARATH	300-312	2	- B:226-238

(no "Exon" information available for 3APZ)

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:299
 aligned with SPS3_ARATH | Q5HZ00 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:341
                                    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 
           SPS3_ARATH    82 LDPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRYSMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQRARELAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 422
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhh......------------.hhhhhhhhhhhhhhhh....--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhh----------------.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhh...hhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------POLYPRENYL_SYNT-----------------------------------------------------------------------------------------------------------POLYPRENYL_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3apz A   8 LDPFSLVADELSLLSNKLREMVLAEVP------------GVQGKQFRSTILLLMATALDV--------------TSELRVRQRGIAEITEMIHVASLLHDDV----------------MGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRYSMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQRARELAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 348
                                    17        27      |  -        47        57        67         -    |   87        97       107 |       -       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347 
                                                     34           47                  67             82                        109              126

Chain B from PDB  Type:PROTEIN  Length:299
 aligned with SPS3_ARATH | Q5HZ00 from UniProtKB/Swiss-Prot  Length:422

    Alignment length:340
                                    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       382       392       402       412       422
           SPS3_ARATH    83 DPFSLVADELSLLSNKLREMVLAEVPKLASAAEYFFKRGVQGKQFRSTILLLMATALNVRVPEALIGESTDIVTSELRVRQRGIAEITEMIHVASLLHDDVLDDADTRRGVGSLNVVMGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRYSMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQRARELAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 422
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh......------------hhhhhhhhhhhhhhhhhh...--------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh---------------..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..hhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------POLYPRENYL_SYNT-----------------------------------------------------------------------------------------------------------POLYPRENYL_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3apz B   9 DPFSLVADELSLLSNKLREMVLAEVP------------GVQGKQFRSTILLLMATALDV--------------TSELRVRQRGIAEITEMIHVASLLHDDVL---------------MGNKMSVLAGDFLLSRACGALAALKNTEVVALLATAVEHLVTGETMEITSSTEQRYSMDYYMQKTYYKTASLISNSCKAVAVLTGQTAEVAVLAFEYGRNLGLAFQLIDDILDFTGTSASLGKGSLSDIRHGVITAPILFAMEEFPQLREVVDQVEKDPRNVDIALEYLGKSKGIQRARELAMEHANLAAAAIGSLPETDNEDVKRSRRALIDLTHRVITRNK 348
                                    18        28     |   -        48        58        |-         -   |    88        98       108 |       -       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348
                                                    34           47                  67             82                         110             126

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 '\|'

(no "SCOP Domain" information available for 3APZ)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (SPS3_ARATH | Q5HZ00)

molecular function
	GO:0052924	all-trans-nonaprenyl-diphosphate synthase (geranylgeranyl-diphosphate specific) activity	Catalysis of the reaction: geranylgeranyl diphosphate + 5 isopentenyl diphosphate = 5 diphosphate + all-trans-nonaprenyl diphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004659	prenyltransferase activity	Catalysis of the transfer of a prenyl group from one compound (donor) to another (acceptor).
	GO:0050347	trans-octaprenyltranstransferase activity	Catalysis of the reaction: all-trans-octaprenyl diphosphate + isopentenyl diphosphate = all-trans-nonaprenyl diphosphate + diphosphate.
	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:0009793	embryo development ending in seed dormancy	The process whose specific outcome is the progression of the embryo over time, from zygote formation to the end of seed dormancy. An example of this process is found in Arabidopsis thaliana.
	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.
	GO:0006744	ubiquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.
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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	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 Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3apz)

	Sites
(no "Sites" information available for 3apz)

	Cis Peptide Bonds
		Val A:33 - Pro A:34	[ RasMol ]
		Val B:33 - Pro B:34	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3apz
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	2.5.1.30
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	SPS3_ARATH \| Q5HZ00	:	3aq0

Description

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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