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Description

Title :   CO-CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE (ISPF) FROM E. COLI INVOLVED IN MEVALONATE-INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CMP/MECDP/MN2+

Authors :   S. B. Richard, J. L. Ferrer, M. E. Bowman, A. M. Lillo, C. N. Tetzlaff, D. E J. P. Noel

Date :   18 Dec 01 (Deposition) - 18 Jun 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Isoprenoids, Deoxyxylulose/Methyl-Erythritol-Phosphate Pathway, Cyclodiphosphate, Mep, Ygbb, Ispf, Mecdp, 2-C-Methyl-D-Erythritol-2, 4-Cyclodiphosphate Synthase, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Richard, J. L. Ferrer, M. E. Bowman, A. M. Lillo, C. N. Tetzlaff, D. E. Cane, J. P. Noel
Structure And Mechanism Of 2-C-Methyl-D-Erythritol 2, 4-Cyclodiphosphate Synthase. An Enzyme In The Mevalonate-Independent Isoprenoid Biosynthetic Pathway.
J. Biol. Chem. V. 277 8667 2002
PubMed-ID: 11786530 | Reference-DOI: 10.1074/JBC.C100739200
(for further references see the PDB file header)

Compounds

Molecule 1 - 2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PHIS8
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ISPF
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	MECPS

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 7)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	C5P	1	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
2	CDI	1	Ligand/Ion	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
3	MN	1	Ligand/Ion	MANGANESE (II) ION
4	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	C5P	3	Ligand/Ion	CYTIDINE-5'-MONOPHOSPHATE
2	CDI	3	Ligand/Ion	2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
3	MN	-1	Ligand/Ion	MANGANESE (II) ION
4	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:8 , HIS A:10 , HIS A:42 , CDI A:301	BINDING SITE FOR RESIDUE MN A 401
2	AC2	SOFTWARE	ASP A:56 , GLY A:58 , ALA A:100 , PRO A:103 , LYS A:104 , MSE A:105 , LEU A:106 , ALA A:131 , THR A:132 , THR A:133 , GLU A:135 , CDI A:301	BINDING SITE FOR RESIDUE C5P A 201
3	AC3	SOFTWARE	ASP A:8 , HIS A:10 , ALA A:33 , HIS A:34 , SER A:35 , HIS A:42 , ILE A:57 , PRO A:62 , C5P A:201 , MN A:401 , HOH A:422	BINDING SITE FOR RESIDUE CDI A 301

SS Bonds (0, 0)

(no "SS Bond" information available for 1KNJ)

Cis Peptide Bonds (1, 1)

Asymmetric Unit

No.	Residues
1	Ala A:102	-	Pro A:103

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1KNJ)

PROSITE Motifs (1, 1)

Asymmetric Unit (1, 1)

	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	1	A:35-50

Biological Unit 1 (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

Exons (0, 0)

(no "Exon" information available for 1KNJ)

Sequences/Alignments

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
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Chain A from PDB  Type:PROTEIN  Length:156
 aligned with ISPF_ECOLI | P62617 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      
           ISPF_ECOLI     1 MRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
               SCOP domains d1knja_ A: 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase IspF                                                                                         SCOP domains
               CATH domains -1knjA00 A:2-156  [code=3.30.1330.50, no name defined]                                                                                                       CATH domains
               Pfam domains YgbB-1knjA01 A:1-156                                                                                                                                         Pfam domains
         Sec.struct. author .eeeeeeeeee......eee..eee............hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh..eeeeeeeeee........hhhhhhhhhhhhh..hhh.eeeeee....hhhhhh..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------ISPF            ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1knj A   1 mRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTIIAQAPKmLPHIPQmRVFIAEDLGCHmDDVNVKATTTEKLGFTGRGEGIACEAVALLIK 156
                            |       10        20        30        40        50        60        70        80        90       100    |  110 |     120   |   130       140       150      
                            |                                                                                                     105-MSE  |         124-MSE                            
                            1-MSE                                                                                                        112-MSE

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

Asymmetric 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 [TaxId: 562] (13)

d1knja_

CATH Domains (1, 1)

Asymmetric 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. Organism_taxid: 562. (9)

1knjA00

A:2-156

Pfam Domains (1, 1)

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: no clan defined [family: YgbB] (24)

Family: YgbB (24)

Escherichia coli (strain K12) (8)

YgbB-1knjA01

A:1-156

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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		Ala A:102 - Pro A:103	[ RasMol ]

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	ISPF_ECOLI \| P62617	:	1gx1 1h47 1h48 1jy8 1knk 1u3l 1u3p 1u40 1u43 1yqn 2amt 2gzl 3elc 3eor 3ern 3esj 3fba

Related Entries Specified in the PDB File

1knk	CRYSTAL STRUCTURE OF 2-C-METHYL-D-ERYTHRITOL 2,4- CYCLODIPHOSPHATE SYNTHASE (ISPF) FROM E. COLI INVOLVED IN MEVALONATE-INDEPENDENT ISOPRENOID BIOSYNTHESIS