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Title :   CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CDP-ME AND MG2+

Authors :   S. B. Richard, M. E. Bowman, W. Kwiatkowski, I. Kang, C. Chow, A. Lillo, D J. P. Noel

Date :   14 May 01 (Deposition) - 14 Nov 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.82

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

Keywords :   Ygbp, Cytidylyltransferase, Deoxyxylulose-5-Phosphate Pathway (Dxp), Isoprenoid Biosynthesis, Cdpme, Mg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. B. Richard, M. E. Bowman, W. Kwiatkowski, I. Kang, C. Chow, A. M. Lillo, D. E. Cane, J. P. Noel
Structure Of 4-Diphosphocytidyl-2-C- Methylerythritol Synthetase Involved In Mevalonate- Independent Isoprenoid Biosynthesis.
Nat. Struct. Biol. V. 8 641 2001
PubMed-ID: 11427897 | Reference-DOI: 10.1038/89691

Molecule 1 - 4-DIPHOSPHOCYTIDYL-2-C-METHYLERYTHRITOL SYNTHETASE
	Chains	:	A
	EC Number	:	2.7.7.-
	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	:	ISPD
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CDM	1	Ligand/Ion	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CDM	2	Ligand/Ion	4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:20 , CDM A:1001	BINDING SITE FOR RESIDUE MG A 1002
2	AC2	SOFTWARE	PRO A:13 , ALA A:14 , ALA A:15 , GLY A:16 , ARG A:20 , LYS A:27 , GLY A:82 , ASP A:83 , GLU A:84 , ARG A:85 , SER A:88 , ASP A:106 , ALA A:107 , ALA A:108 , ARG A:109 , ASP A:139 , THR A:140 , ARG A:157 , ALA A:163 , THR A:189 , LYS A:213 , THR A:215 , MG A:1002	BINDING SITE FOR RESIDUE CDM A 1001

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

Asymmetric Unit

No.	Residues
1	Thr A:165	-	Pro A:166

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_ECOLI	102-109	1	A:102-109

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_ECOLI	102-109	2	A:102-109

(no "Exon" information available for 1INI)

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:225
 aligned with ISPD_ECOLI | Q46893 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223     
           ISPD_ECOLI     4 THLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLT 228
               SCOP domains d1inia_ A: 4-diphosphocytidyl-2C-methyl-D-erythritol (CDP-me) synthase (IspD, YgbP)                                                                                                                                               SCOP domains
               CATH domains 1iniA00 A:4-228 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee............hhhh.ee..eehhhhhhhhhhh...eeeeeeee.....hhhhhhhhhh..eeeee...hhhhhhhhhhh......eeee........hhhhhhhhhhhhhh....eeeeee....eeee......eeeee.....eeeeeeeeeehhhhhhhhhhhhhh.....hhhhhhhhh....eeee.........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------ISPD    ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ini A   4 THLDVCAVVPAAGFGRRMQTECPKQYLSIGNQTILEHSVHALLAHPRVKRVVIAISPGDSRFAQLPLANHPQITVVDGGDERADSVLAGLKAAGDAQWVLVHDAARPCLHQDDLARLLALSETSRTGGILAAPVRDTMKRAEPGKNAIAHTVDRNGLWHALTPQFFPRELLHDCLTRALNEGATITDEASALEYCGFHPQLVEGRADNIKVTRPEDLALAEFYLT 228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Complex (3881)

Topology: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Homologous Superfamily: Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A (231)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (3)

1iniA00

A:4-228

(no "Pfam Domain" information available for 1INI)

Asymmetric Unit(hide GO term definitions)

Chain A (ISPD_ECOLI | Q46893)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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: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.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	ISPD_ECOLI \| Q46893	:	1h3m 1i52 1inj 1vgt 1vgu 3n9w

1i52	CRYSTAL STRUCTURE OF 4-DIPHOSPHOCYTIDYL-2-C- METHYLERYTHRITOL (CDP-ME) SYNTHASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS, COMPLEXED WITH CTP AND MG2+
1inj	CRYSTAL STRUCTURE OF THE APO FORM OF 4-DIPHOSPHOCYTIDYL-2-C -METHYLERYTHRITOL (CDP-ME) SYNTHETASE (YGBP) INVOLVED IN MEVALONATE INDEPENDENT ISOPRENOID BIOSYNTHESIS

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