2JGR - JenaLib

Title :   CRYSTAL STRUCTURE OF YEGS IN COMPLEX WITH ADP

Authors :   H. M. Bakali, M. D. Herman, K. A. Johnson, A. A. Kelly, A. Wieslander, B. M. Hallberg, P. Nordlund

Date :   14 Feb 07 (Deposition) - 15 May 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.65

Chains :   Asym./Biol. Unit : A

Keywords :   Phosphatidylglycerole Kinase, Transferase, Lipid Kinase, Pyrrophosphate, Hypothetical Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. M. Bakali, M. D. Herman, K. A. Johnson, A. A. Kelly, A. Wieslander, B. M. Hallberg, P. Nordlund
Crystal Structure Of Yegs, A Homologue To The Mammalian Diacylglycerol Kinases, Reveals A Novel Regulatory Metal Binding Site.
J. Biol. Chem. V. 282 19644 2007
PubMed-ID: 17351295 | Reference-DOI: 10.1074/JBC.M604852200

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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:261
 aligned with YEGS_ECOLI | P76407 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
           YEGS_ECOLI     4 FPASLLILNGKSTDNLPLREAIMLLREEGMTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDMAQVNKQTCFINMATGGFGTRITTETPEKLKAALGSVSYIIHGLMRMDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFTGDEILPALVSTLKSDEDNPNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLR 299
               SCOP domains d2jgra1 A:4-229 Lipid kinase YegS                                                                                                                                                                                                                ------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhh........eeeeee....hhhhhhh....hhhhhhhhhhhh.eeeeeeeee...eee..eeeee...--------------------............eeeeeee..eeeeeee.eeeee...ee...ee...........eeeeee...---------------...eeeeee.eeeeeeeeeeeeee..eeeeeeeeeeeeeeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jgr A   4 FPASLLILNGKSTDNLPLREAImLLREEGmTIHVRVTWEKGDAARYVEEARKFGVATVIAGGGDGTINEVSTALIQCEGDDIPALGILPLGTANDFATSVGIPEALDKALKLAIAGDAIAIDmAQVNKQTCFINmATGGFGT--------------------IHGLmRmDTLQPDRCEIRGENFHWQGDALVIGIGNGRQAGGGQQLCPNALINDGLLQLRIFTGD---------------NPNIIEGASSWFDIQAPHDITFNLDGEPLSGQNFHIEILPAALRCRLPPDCPLLR 299
                                    13        23  |     33        43        53        63        73        83        93       103       113       123  |    133    |  143 |       -         -  |   |173       183       193       203       213       223     |   -         - |     253       263       273       283       293      
                                                 26-MSE 33-MSE                                                                                      126-MSE     138-MSE145                  166   | |                                                      229             245                                                      
                                                                                                                                                                                                170-MSE                                                                                                                             
                                                                                                                                                                                                  172-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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (YEGS_ECOLI | P76407)

molecular function
	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:0001727	lipid kinase activity	Catalysis of the phosphorylation of a simple or complex lipid.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0046834	lipid phosphorylation	The process of introducing one or more phosphate groups into a lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents.
	GO:0008654	phospholipid biosynthetic process	The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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