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Title :   CRYSTAL STRUCTURE OF 2C-METHYL-D-ERYTHRITOL 2,4-CLYCODIPHOSPHATE SYNTHASE COMPLEXED WITH LIGAND

Authors :   W. N. Hunter, N. L. Ramsden, V. Ulaganathan

Date :   22 Sep 08 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Mecdp-Synthase, Isoprene Biosynthesis, Lyase, Magnesium, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. L. Ramsden, L. Buetow, A. Dawson, L. A. Kemp, V. Ulaganathan, R. Brenk, G. Klebe, W. N. Hunter
A Structure-Based Approach To Ligand Discovery For 2C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase: A Target For Antimicrobial Therapy
J. Med. Chem. V. 52 2531 2009
PubMed-ID: 19320487 | Reference-DOI: 10.1021/JM801475N
(for further references see the PDB file header)

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A, B, C
	EC Number	:	4.6.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ISPF
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	MECPS, MECDP-SYNTHASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	F01	3	Ligand/Ion	4-AMINO-1-[(2R,3R,4S,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)OXOLAN-2-YL]-5-FLUORO-PYRIMIDIN-2-ONE
2	GPP	1	Ligand/Ion	GERANYL DIPHOSPHATE
3	ZN	3	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , HIS A:10 , HIS A:42	BINDING SITE FOR RESIDUE ZN A 801
2	AC2	SOFTWARE	ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , ASP C:56 , GLY C:58	BINDING SITE FOR RESIDUE F01 A 901
3	AC3	SOFTWARE	ASP B:8 , HIS B:10 , HIS B:42	BINDING SITE FOR RESIDUE ZN B 802
4	AC4	SOFTWARE	ASP A:56 , GLY A:58 , ALA B:100 , PRO B:103 , LYS B:104 , MET B:105 , LEU B:106 , ALA B:131 , THR B:132 , THR B:133 , HOH B:929	BINDING SITE FOR RESIDUE F01 B 902
5	AC5	SOFTWARE	ASP C:8 , HIS C:10 , HIS C:42	BINDING SITE FOR RESIDUE ZN C 803
6	AC6	SOFTWARE	ASP B:56 , GLY B:58 , ALA C:100 , PRO C:103 , LYS C:104 , MET C:105 , LEU C:106 , ALA C:131 , THR C:132 , THR C:133	BINDING SITE FOR RESIDUE F01 C 903
7	AC7	SOFTWARE	GLY A:138 , PHE A:139 , ARG A:142 , GLY B:138 , PHE B:139 , ARG B:142 , THR C:134 , GLY C:138 , PHE C:139 , ARG C:142 , HOH C:928	BINDING SITE FOR RESIDUE GPP C 904

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

Asymmetric/Biological Unit

No.	Residues
1	Gly A:16	-	Pro A:17
2	Ala A:102	-	Pro A:103
3	Gly B:16	-	Pro B:17
4	Ala B:102	-	Pro B:103
5	Gly C:16	-	Pro C:17
6	Ala C:102	-	Pro C:103

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

Asymmetric/Biological Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPF	PS01350	2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature.	ISPF_ECOLI	35-50	3	A:35-50 B:35-50 C:35-50

(no "Exon" information available for 3ELC)

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:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3elca_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3elcA00 A:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eee..eee.....ee.....hhhhhhhhhhhhhhh...hhhhhh...hhhhh..hhhhhhhhhhhhhhhh..eeeeeeeeee........hhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elc A   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain B from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3elcb_ B: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3elcB00 B:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elc B   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

Chain C from PDB  Type:PROTEIN  Length:157
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:157
                             1                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       
           ISPF_ECOLI     - -MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d3elcc_ C: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3elcC00 C:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeee..eee..eee...eee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhh...eeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3elc C   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Bacillus chorismate mutase-like (324)

Superfamily: IpsF-like (56)

Family: IpsF-like (35)

Protein domain: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF (27)

Escherichia coli K-12 [TaxId: 83333] (5)

1a	d3elca_	A:
1b	d3elcb_	B:
1c	d3elcc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 60s Ribosomal Protein L30; Chain: A; (235)

Homologous Superfamily: [code=3.30.1330.50, no name defined] (46)

Escherichia coli k-12. Organism_taxid: 83333. Strain: k12. (4)

1a	3elcA00	A:0-156
1b	3elcB00	B:0-156
1c	3elcC00	C:0-156

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (ISPF_ECOLI | P62617)

molecular function
	GO:0008685	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	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:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
	GO:0006744	ubiquinone biosynthetic process	The chemical reactions and pathways resulting in the formation of ubiquinone, a lipid-soluble electron-transporting coenzyme.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:102 - Pro A:103	[ RasMol ]
		Ala B:102 - Pro B:103	[ RasMol ]
		Ala C:102 - Pro C:103	[ RasMol ]
		Gly A:16 - Pro A:17	[ RasMol ]
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		Gly C:16 - Pro C:17	[ RasMol ]

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	3elc
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Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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