1UEK - JenaLib

Title :   CRYSTAL STRUCTURE OF 4-(CYTIDINE 5'-DIPHOSPHO)-2C-METHYL-D-ERYTHRITOL KINASE

Authors :   T. Wada, S. Kuramitsu, S. Yokoyama, J. R. H. Tame, S. Y. Park, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   17 May 03 (Deposition) - 17 Jun 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Non-Mevalonate Pathway, Ghmp Superfamily, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Wada, T. Kuzuyama, S. Satoh, S. Kuramitsu, S. Yokoyama, S. Unzai, J. R. Tame, S. Y. Park
Crystal Structure Of 4-(Cytidine 5'-Diphospho)-2-C-Methyl-D-Erythritol Kinase, An Enzyme In The Non-Mevalonate Pathway Of Isoprenoid Synthesis.
J. Biol. Chem. V. 278 30022 2003
PubMed-ID: 12771135 | Reference-DOI: 10.1074/JBC.M304339200
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:268
 aligned with ISPE_THET8 | P83700 from UniProtKB/Swiss-Prot  Length:275

    Alignment length:268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        
           ISPE_THET8     1 MERLAPAKVNLGLSVRFRREDGYHELHTLFAPFSLADRLVVEPVSSGLHFQGPYGRENLAYRAASLYLEAAGQPGGVRILLEKRIPEGAGLGGGSSDAAQVLLALQALYPAEVDLFALARTLGADVPFFLLGRGAEARGVGERLKPLALPPVPAVVFFPGLRVPTPLVYRAVRPEDFGPDLPVEAILEALARGEEPPYWNSLEGPAFRLFPELKEVRGRMRALGLRGVLMSGSGSAFFGLAEGPDHARRAAEALRAWGRAWAGTLGGG 268
               SCOP domains d1ueka1 A:1-148 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                                                        d1ueka2 A:149-268 4-(cytidine 5'-diphospho)-2C-methyl-D-erythritol kinase IspE                                           SCOP domains
               CATH domains 1uekA01 A:1-148  [code=3.30.230.10, no name defined]                                                                                                ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -----------------------------------------------------------------------------GHMP_kinases_N-1uekA01 A:78-133                         -------------------------------------------------GHMP_kinases_C-1uekA02 A:183-260                                              -------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeeeeee...eeee..hhhhhhhhhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhh.eeeee....eeeee....eeeeeee.....hhhhhhhh.hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeee......eeee..hhhhhhhhhhhhh...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uek A   1 MERLAPAKVNLGLSVRFRREDGYHELHTLFAPFSLADRLVVEPVSSGLHFQGPYGRENLAYRAASLYLEAAGQPGGVRILLEKRIPEGAGLGGGSSDAAQVLLALQALYPAEVDLFALARTLGADVPFFLLGRGAEARGVGERLKPLALPPVPAVVFFPGLRVPTPLVYRAVRPEDFGPDLPVEAILEALARGEEPPYWNSLEGPAFRLFPELKEVRGRMRALGLRGVLMSGSGSAFFGLAEGPDHARRAAEALRAWGRAWAGTLGGG 268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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 (1, 1)

Pfam Domains (2, 2)

Gene Ontology (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ISPE_THET8 | P83700)

molecular function
	GO:0050515	4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity	Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + 2 H(+).
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1uek)

	Sites
(no "Sites" information available for 1uek)

	Cis Peptide Bonds
		Gly A:234 - Ser A:235	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1uek
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ISPE_THET8 \| P83700
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.1.148
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description