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NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   NMR SOLUTION STRUCTURE OF E. COLI DIACYLGLYCEROL KINASE (DAGK) IN DPC MICELLES

Authors :   W. D. Van Horn, H. Kim, C. D. Ellis, A. Hadziselimovic, E. S. Sulistijo, M. D. Karra, C. Tian, F. D. Sonnichsen, C. R. Sanders

Date :   06 Jan 09 (Deposition) - 07 Jul 09 (Release) - 07 Jul 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B,C  (16x)

Keywords :   Membrane Protein, Solution Nmr, Kinase, Dagk, Cell Inner Membrane, Cell Membrane, Membrane, Phospholipid Biosynthesis, Transferase, Transmembrane (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. D. Van Horn, H. J. Kim, C. D. Ellis, A. Hadziselimovic, E. S. Sulistijo, M. D. Karra, C. Tian, F. D. Sonnichsen, C. R. Sanders
Solution Nuclear Magnetic Resonance Structure Of Membrane-Integral Diacylglycerol Kinase
Science V. 324 1726 2009
PubMed-ID: 19556511 | Reference-DOI: 10.1126/SCIENCE.1171716
(for further references see the PDB file header)

Molecule 1 - DIACYLGLYCEROL KINASE
	Chains	:	A, B, C
	EC Number	:	2.7.1.107
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PSD004
	Gene	:	DGKA, B4042, JW4002
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Synonym	:	DAGK, DIGLYCERIDE KINASE, DGK


NMR Structure (16x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KDC)

(no "Site" information available for 2KDC)

(no "SS Bond" information available for 2KDC)

(no "Cis Peptide Bond" information available for 2KDC)

(no "SAP(SNP)/Variant" information available for 2KDC)

NMR Structure (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAGK_PROKAR	PS01069	Prokaryotic diacylglycerol kinase signature.	KDGL_ECOLI	70-81	3	A:69-80 B:69-80 C:69-80

(no "Exon" information available for 2KDC)

NMR Structure

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:121
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           KDGL_ECOLI     2 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kdcA00 A:1-121 Diacylglycerol kinase domain                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kdc A   1 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           KDGL_ECOLI     2 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kdcB00 B:1-121 Diacylglycerol kinase domain                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kdc B   1 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:121
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           KDGL_ECOLI     2 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kdcC00 C:1-121 Diacylglycerol kinase domain                                                                              CATH domains
           Pfam domains (1) -------------DAGK_prokar-2kdcC01 C:14-117                                                                            ---- Pfam domains (1)
           Pfam domains (2) -------------DAGK_prokar-2kdcC02 C:14-117                                                                            ---- Pfam domains (2)
           Pfam domains (3) -------------DAGK_prokar-2kdcC03 C:14-117                                                                            ---- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2kdc C   1 ANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 '\|'

(no "SCOP Domain" information available for 2KDC)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Diacylglycerol kinase fold (1)

Homologous Superfamily: Diacylglycerol kinase domain (1)

Escherichia coli. Organism_taxid: 83333. (1)

1a	2kdcA00	A:1-121
1b	2kdcB00	B:1-121
1c	2kdcC00	C:1-121

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: DAGK_prokar] (1)

Family: DAGK_prokar (1)

Escherichia coli (strain K12) (1)

1a	DAGK_prokar-2kdcC01	C:14-117
1b	DAGK_prokar-2kdcC02	C:14-117
1c	DAGK_prokar-2kdcC03	C:14-117

NMR Structure(hide GO term definitions)

Chain A,B,C (KDGL_ECOLI | P0ABN1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004143	diacylglycerol kinase activity	Catalysis of the reaction: NTP + 1,2-diacylglycerol = NDP + 1,2-diacylglycerol-3-phosphate.
	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: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:0006654	phosphatidic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidic acid, any derivative of glycerol phosphate in which both the remaining hydroxyl groups of the glycerol moiety are esterified with fatty acids.
	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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

NMR Structure
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