3AQB - 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)

Title :   M. LUTEUS B-P 26 HETERODIMERIC HEXAPRENYL DIPHOSPHATE SYNTHASE IN COMPLEX WITH MAGNESIUM

Authors :   D. Sasaki, M. Fujihashi, N. Okuyama, Y. Kobayashi, M. Noike, T. Koyama,

Date :   28 Oct 10 (Deposition) - 10 Nov 10 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Prenyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Sasaki, M. Fujihashi, N. Okuyama, Y. Kobayashi, M. Noike, T. Koyama K. Miki
Crystal Structure Of Heterodimeric Hexaprenyl Diphosphate Synthase From Micrococcus Luteus B-P 26 Reveals That The Small Subunit Is Directly Involved In The Product Chain Length Regulation.
J. Biol. Chem. V. 286 3729 2011
PubMed-ID: 21068379 | Reference-DOI: 10.1074/JBC.M110.147991

Molecule 1 - COMPONENT A OF HEXAPRENYL DIPHOSPHATE SYNTHASE
	Chains	:	A, C
	EC Number	:	2.5.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-32 EK/LIC
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HEXS-A
	Organism Scientific	:	MICROCOCCUS LUTEUS
	Organism Taxid	:	1270
	Strain	:	B-P 26
	Synonym	:	HEXAPRENYL DIPHOSPHATE SYNTHASE SMALL SUBUNIT

Molecule 2 - COMPONENT B OF HEXAPRENYL DIPHOSPHATE SYNTHASE
	Chains	:	B, D
	EC Number	:	2.5.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-30 EK/LIC
	Expression System Strain	:	ROSETTA2(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HEXS-B
	Organism Scientific	:	MICROCOCCUS LUTEUS
	Organism Taxid	:	1270
	Strain	:	B-P 26
	Synonym	:	HEXAPRENYL DIPHOSPHATE SYNTHASE LARGE SUBUNIT

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP B:84 , ASP B:88	BINDING SITE FOR RESIDUE MG B 326
2	AC2	SOFTWARE	ASP B:211	BINDING SITE FOR RESIDUE MG B 327
3	AC3	SOFTWARE	ASP D:84 , ASP D:88 , HOH D:366	BINDING SITE FOR RESIDUE MG D 326
4	AC4	SOFTWARE	ASP D:211 , ASP D:230 , HOH D:348 , HOH D:368	BINDING SITE FOR RESIDUE MG D 327
5	AC5	SOFTWARE	MET D:1 , ILE D:2 , ARG D:153 , HOH D:337	BINDING SITE FOR RESIDUE CL D 328

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

Asymmetric Unit

No.	Residues
1	Gln A:85	-	Pro A:86
2	Tyr B:156	-	Pro B:157
3	Gln C:85	-	Pro C:86
4	Tyr D:156	-	Pro D:157

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	HEXB_MICLU	81-95	2	B:81-95 D:81-95
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	HEXB_MICLU	203-215	2	B:203-215 D:203-215

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	HEXB_MICLU	81-95	1	B:81-95 -
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	HEXB_MICLU	203-215	1	B:203-215 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	POLYPRENYL_SYNTHASE_1	PS00723	Polyprenyl synthases signature 1.	HEXB_MICLU	81-95	1	- D:81-95
2	POLYPRENYL_SYNTHASE_2	PS00444	Polyprenyl synthases signature 2.	HEXB_MICLU	203-215	1	- D:203-215

(no "Exon" information available for 3AQB)

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:135
 aligned with HEXA_MICLU | O66127 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:135
                             1                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129     
           HEXA_MICLU     - -MRYLHKIELELNRLTSRYPFFKKIAFDAEIIKLVDDLNVDENVKCAIVAIDTSMRMQDFINEDNKDSFVLSTDVLSALFYKYLSQPFYQHDFLVLTDCVSRINELKSIRATITDEIALHNINKQIHYMFIQPYM 134
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh........hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqb A   0 MMRYLHKIELELNRLTSRYPFFKKIAFDAEIIKLVDDLNVDENVKCAIVAIDTSMRMQDFINEDNKDSFVLSTDVLSALFYKYLSQPFYQHDFLVLTDCVSRINELKSIRATITDEIALHNINKQIHYMFIQPYM 134
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain B from PDB  Type:PROTEIN  Length:321
 aligned with HEXB_MICLU | O66129 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:321
                                    14        24        34        44        54        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 
           HEXB_MICLU     5 SYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQDSNIKDYLEEIHEKMLKRVY 325
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------POLYPRENYL_SYNT-----------------------------------------------------------------------------------------------------------POLYPRENYL_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqb B   5 SYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQDSNIKDYLEEIHEKMLKRVY 325
                                    14        24        34        44        54        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

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with HEXA_MICLU | O66127 from UniProtKB/Swiss-Prot  Length:143

    Alignment length:135
                             1                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129     
           HEXA_MICLU     - -MRYLHKIELELNRLTSRYPFFKKIAFDAEIIKLVDDLNVDENVKCAIVAIDTSMRMQDFINEDNKDSFVLSTDVLSALFYKYLSQPFYQHDFLVLTDCVSRINELKSIRATITDEIALHNINKQIHYMFIQPYM 134
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqb C   0 MMRYLHKIELELNRLTSRYPFFKKIAFDAEIIKLVDDLNVDENVKCAIVAIDTSMRMQDFINEDNKDSFVLSTDVLSALFYKYLSQPFYQHDFLVLTDCVSRINELKSIRATITDEIALHNINKQIHYMFIQPYM 134
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain D from PDB  Type:PROTEIN  Length:325
 aligned with HEXB_MICLU | O66129 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:325
                                    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       300       310       320     
           HEXB_MICLU     1 MIALSYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQDSNIKDYLEEIHEKMLKRVY 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------POLYPRENYL_SYNT-----------------------------------------------------------------------------------------------------------POLYPRENYL_SY-------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aqb D   1 MIALSYKAFLNPYIIEVEKRLYECIQSDSETINKAAHHILSSGGKRVRPMFVLLSGFLNDTQKDDLIRTAVSLELVHMASLVHDDYIDNSDMRRGNTSVHIAFDKDTAIRTGHFLLARALQNIATINNSKFHQIFSKTILEVCFGEFDQMADRFNYPVSFTAYLRRINRKTAILIEASCHLGALSSQLDEQSTYHIKQFGHCIGMSYQIIDDILDYTSDEATLGKPVGSDIRNGHITYPLMAAIANLKEQDDDKLEAVVKHLTSTSDDEVYQYIVSQVKQYGIEPAELLSRKYGDKAKYHLSQLQDSNIKDYLEEIHEKMLKRVY 325
                                    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       300       310       320

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 3AQB)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,C (HEXA_MICLU | O66127)

molecular function
	GO:0036423	hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity	Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate = 3 diphosphate + all-trans-hexaprenyl diphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
biological process
	GO:0009234	menaquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

Chain B,D (HEXB_MICLU | O66129)

molecular function
	GO:0036423	hexaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific) activity	Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 3 isopentenyl diphosphate = 3 diphosphate + all-trans-hexaprenyl diphosphate.
	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: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.
	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
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.
	GO:0009234	menaquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.

Asymmetric Unit
	Complete Structure
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	Cis Peptide Bonds
		Gln A:85 - Pro A:86	[ RasMol ]
		Gln C:85 - Pro C:86	[ RasMol ]
		Tyr B:156 - Pro B:157	[ RasMol ]
		Tyr D:156 - Pro D:157	[ RasMol ]

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

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	3aqb
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	HEXA_MICLU \| O66127
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	HEXB_MICLU \| O66129
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	2.5.1.33
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	HEXA_MICLU \| O66127	:	3aqc
	HEXB_MICLU \| O66129	:	3aqc

Description

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Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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