3EOR - JenaLib

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

Authors :   W. N. Hunter, N. L. Ramsden, A. Dawson

Date :   29 Sep 08 (Deposition) - 25 Aug 09 (Release) - 25 Aug 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)

Keywords :   Mecdp-Synthase, Lysase, 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)

Compounds

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A
	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

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , HIS A:10 , HIS A:42 , NA A:801 , NA A:802	BINDING SITE FOR RESIDUE ZN A 800
2	AC2	SOFTWARE	ASP A:8 , ZN A:800	BINDING SITE FOR RESIDUE NA A 801
3	AC3	SOFTWARE	SER A:35 , ZN A:800	BINDING SITE FOR RESIDUE NA A 802
4	AC4	SOFTWARE	ALA A:100 , PRO A:103 , LYS A:104 , MET A:105 , LEU A:106 , ALA A:131 , HOH A:928 , HOH A:935	BINDING SITE FOR RESIDUE CFV A 901
5	AC5	SOFTWARE	GLY A:138 , PHE A:139 , ARG A:142 , GLU A:149	BINDING SITE FOR RESIDUE GPP A 902

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

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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 d3eora_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                          SCOP domains
               CATH domains 3eorA00 A:0-156  [code=3.30.1330.50, no name defined]                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee......eee..eee............hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eor A   0 EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (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.

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