1W55 - JenaLib

Title :   STRUCTURE OF THE BIFUNCTIONAL ISPDF FROM CAMPYLOBACTER JEJUNI

Authors :   M. Gabrielsen, C. S. Bond, W. N. Hunter

Date :   05 Aug 04 (Deposition) - 04 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (6x)

Keywords :   Bifunctional Enzyme, Biosynthetic Pathway, Isoprenoids, Bifunctional, Nonmevalonate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Gabrielsen, C. S. Bond, I. Hallyburton, S. Hecht, A. Bacher, W. Eisenreich, F. Rohdich, W. N. Hunter
Hexameric Assembly Of The Bifunctional Methylerythritol 2, 4-Cyclodiphosphate Synthase And Protein-Protein Associations In The Deoxy-Xylulose-Dependent Pathway Of Isoprenoid Precursor Biosynthesis
J. Biol. Chem. V. 279 52753 2004
PubMed-ID: 15466439 | Reference-DOI: 10.1074/JBC.M408895200

Compounds

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:217 , THR A:341 , C A:1372 , HOH A:2226 , HOH A:2244 , HOH A:2245	BINDING SITE FOR RESIDUE MG A1371
2	AC2	SOFTWARE	HIS A:243 , ASP A:265 , GLY A:267 , ALA A:309 , PRO A:312 , LYS A:313 , LEU A:314 , LYS A:315 , LYS A:318 , ALA A:340 , THR A:341 , THR A:342 , MG A:1371 , HOH A:2168 , HOH A:2240 , HOH A:2241 , HOH A:2242 , HOH A:2244 , HOH A:2245	BINDING SITE FOR RESIDUE C A1372
3	AC3	SOFTWARE	LEU A:9 , ALA A:10 , ALA A:11 , THR A:53 , GLY A:73 , ASP A:74 , THR A:75 , ARG A:76 , SER A:79 , ASP A:96 , VAL A:97 , ARG A:139 , LYS A:191 , HOH A:2048 , HOH A:2112 , HOH A:2246 , HOH A:2247 , HOH A:2248	BINDING SITE FOR RESIDUE C A1373
4	AC4	SOFTWARE	PHE A:216 , MET A:308 , GLY A:347 , PHE A:348 , ARG A:351 , HOH A:2228	BINDING SITE FOR RESIDUE GPP A1374
5	AC5	SOFTWARE	ASP A:96 , ARG A:99 , ASP A:128 , THR A:129 , ILE A:145 , THR A:167 , LYS A:191 , HOH A:2112	BINDING SITE FOR RESIDUE EDO A1375

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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
	(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:369
 aligned with ISPDF_CAMJE | Q9PM68 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:369
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361         
          ISPDF_CAMJE     2 SEMSLIMLAAGNSTRFNTKVKKQFLRLGNDPLWLYATKNLSSFYPFKKIVVTSSNITYMKKFTKNYEFIEGGDTRAESLKKALELIDSEFVMVSDVARVLVSKNLFDRLIENLDKADCITPALKVADTTLFDNEALQREKIKLIQTPQISKTKLLKKALDQNLEFTDDSTAIAAMGGKIWFVEGEENARKLTFKEDLKKLDLPTPSFEIFTGNGFDVHEFGENRPLLLAGVQIHPTMGLKAHSDGDVLAHSLTDAILGAAGLGDIGELYPDTDMKFKNANSMELLKQAYDKVREIGFELINIDICVMAQSPKLKDFKQAMQSNIAHTLDLDEFRINVKATTTEKLGFIGRKEGMAVLSSVNLKYFDWTR 370
               SCOP domains -d1w55a1 A:3-207 IspD/IspF bifunctional enzyme, CDP-me synthase domain                                                                                                                                        d1w55a2 A:208-370 IspD/ispF bifunctional enzyme, MECDP synthase domain                                                                                              SCOP domains
               CATH domains 1w55A01 A:2-208 Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A                                                                                                                                   1w55A02 A:209-370  [code=3.30.1330.50, no name defined]                                                                                                            CATH domains
               Pfam domains --IspD-1w55A01 A:4-203                                                                                                                                                                                    ------YgbB-1w55A02 A:210-366                                                                                                                                       ---- Pfam domains
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhh......eeeee.hhhhhhh.....eeee...hhhhhhhhhhh.....eeeeee......hhhhhhhhhhhhhhh.eeeeee.....eee..eeehhhhh.ee...eeeehhhhhhhh.......hhhhhhhh....eeeee.hhhhh...hhhhhhhh........eeeeeeeeeeeeeee..eee..eeee..eee......hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhhhhhhhhhh.eeeeeeeeeee.....hhhhhhhhhhhhhhhhh.hhh.eeeeee....hhhhhh..eeeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------------------------------ISPF            --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w55 A   2 SEMSLIMLAAGNSTRFNTKVKKQFLRLGNDPLWLYATKNLSSFYPFKKIVVTSSNITYMKKFTKNYEFIEGGDTRAESLKKALELIDSEFVMVSDVARVLVSKNLFDRLIENLDKADCITPALKVADTTLFDNEALQREKIKLIQTPQISKTKLLKKALDQNLEFTDDSTAIAAMGGKIWFVEGEENARKLTFKEDLKKLDLPTPSFEIFTGNGFDVHEFGENRPLLLAGVQIHPTMGLKAHSDGDVLAHSLTDAILGAAGLGDIGELYPDTDMKFKNANSMELLKQAYDKVREIGFELINIDICVMAQSPKLKDFKQAMQSNIAHTLDLDEFRINVKATTTEKLGFIGRKEGMAVLSSVNLKYFDWTR 370
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361

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 (2, 2)

CATH Domains (2, 2)

Pfam Domains (2, 2)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (ISPDF_CAMJE | Q9PM68)

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: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: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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

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