3ZE3 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - DELTA7

Authors :   D. Li, V. E. Pye, J. A. Lyons, L. Vogeley, D. Aragao, M. Caffrey

Date :   03 Dec 12 (Deposition) - 22 May 13 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: D,E,F  (1x)
Biol. Unit 2: A,B,C  (1x)

Keywords :   Transferase, Lipid Metabolism, In Meso Crystallisation, Lipid Cubic Phase, Lipidic Mesophase, Thermostable Mutant, Monoacylglycerol, 7. 8 Mag (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Li, J. A. Lyons, V. E. Pye, L. Vogeley, D. Aragao, C. P. Kenyon, S. T. A. Shah, C. Doherty, M. Aherne, M. Caffrey
Crystal Structure Of The Integral Membrane Diacylglycerol Kinase.
Nature V. 497 521 2013
PubMed-ID: 23676677 | Reference-DOI: 10.1038/NATURE12179

Molecule 1 - DIACYLGLYCEROL KINASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	2.7.1.107
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRCHISB_DGKA_DELTA7
	Expression System Strain	:	WH1061
	Expression System Taxid	:	562
	Expression System Vector	:	PTRCHISB
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Other Details	:	THE WILD-TYPE GENE WAS SYNTHESIZED BASED ON THE DGKA NUCLEOTIDE SEQUENCE OF ESCHERICHIA COLI K12, WITH ADDITIONAL NUCLEOTIDES ENCODING HIS TAG SEQUENCES AT THE N- TERMINUS. SITE-DIRECTED MUTATIONS WERE MADE USING PCR.
	Synonym	:	DAGK, DIGLYCERIDE KINASE, DGK

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:				D	E	F
Biological Unit 2 (1x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 18)

No.	Name	Count	Type	Full Name
1	78M	6	Ligand/Ion	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2	78N	7	Ligand/Ion	(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3	ACT	1	Ligand/Ion	ACETATE ION
4	FLC	1	Ligand/Ion	CITRATE ANION
5	NA	2	Ligand/Ion	SODIUM ION
6	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	78M	4	Ligand/Ion	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2	78N	-1	Ligand/Ion	(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3	ACT	1	Ligand/Ion	ACETATE ION
4	FLC	1	Ligand/Ion	CITRATE ANION
5	NA	-1	Ligand/Ion	SODIUM ION
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 9)

No.	Name	Count	Type	Full Name
1	78M	2	Ligand/Ion	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
2	78N	7	Ligand/Ion	(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3	ACT	-1	Ligand/Ion	ACETATE ION
4	FLC	-1	Ligand/Ion	CITRATE ANION
5	NA	-1	Ligand/Ion	SODIUM ION
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU D:64 , ASP D:107 , HOH D:2044 , SER F:60 , LEU F:64 , HOH F:2024	BINDING SITE FOR RESIDUE NA F1122
02	AC2	SOFTWARE	SER D:60 , SER E:61 , THR E:111 , HOH E:2020	BINDING SITE FOR RESIDUE NA E1122
03	AC3	SOFTWARE	GLU D:28 , GLU D:76 , FLC D:1123 , ACT D:1124	BINDING SITE FOR RESIDUE ZN D1122
04	AC4	SOFTWARE	GLU D:76 , ZN D:1122 , ACT D:1124 , HOH D:2048	BINDING SITE FOR RESIDUE FLC D1123
05	AC5	SOFTWARE	GLU D:28 , GLU D:69 , ASN D:72 , SER D:73 , GLU D:76 , ZN D:1122 , FLC D:1123 , HOH D:2047	BINDING SITE FOR RESIDUE ACT D1124
06	AC6	SOFTWARE	ALA A:13 , ALA A:14 , SER A:17 , 78N A:1123 , 78N A:1124 , SER B:98 , VAL B:101 , LEU B:102 , ILE B:105 , ILE B:110 , 78N B:1123	BINDING SITE FOR RESIDUE 78N B1122
07	AC7	SOFTWARE	ARG A:9 , 78N A:1124 , GLU B:34 , VAL B:65 , GLU B:69 , ALA B:108 , TRP B:112 , ALA B:113 , 78N B:1122	BINDING SITE FOR RESIDUE 78N B1123
08	AC8	SOFTWARE	GLN A:33 , GLU A:34 , 78M A:1126 , TRP C:117 , 78N C:1122 , TRP D:25 , ALA D:29 , ARG D:32 , GLN D:33 , VAL D:36 , HOH D:2017 , HOH D:2049	BINDING SITE FOR RESIDUE 78M D1125
09	AC9	SOFTWARE	78M A:1126 , ALA B:46 , ARG B:55 , HOH B:2010 , ILE C:110 , ILE C:114 , TRP C:117 , SER C:118 , GLN D:33 , 78M D:1125	BINDING SITE FOR RESIDUE 78N C1122
10	BC1	SOFTWARE	TRP A:18 , ARG A:22 , TRP A:25 , ILE A:26 , LEU A:39 , MET A:63 , MET A:66	BINDING SITE FOR RESIDUE 78N A1122
11	BC2	SOFTWARE	ALA A:30 , PHE A:31 , GLU A:34 , GLU A:69 , LEU A:102 , ILE A:105 , HOH A:2012 , ARG D:22 , TRP D:25 , HOH D:2050	BINDING SITE FOR RESIDUE 78M D1126
12	BC3	SOFTWARE	TRP B:47 , HOH B:2006 , HOH B:2008 , LEU D:102 , VAL D:109 , ALA D:113 , HOH D:2018 , HOH D:2043	BINDING SITE FOR RESIDUE 78M D1127
13	BC4	SOFTWARE	LEU A:40 , TRP A:47 , 78M A:1126 , GLU C:34 , GLU C:69 , TRP C:112	BINDING SITE FOR RESIDUE 78N C1123
14	BC5	SOFTWARE	TRP A:117 , GLY B:35 , VAL B:36 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120	BINDING SITE FOR RESIDUE 78M D1128
15	BC6	SOFTWARE	VAL A:42 , ALA A:46 , ARG A:55 , 78N A:1124 , HOH A:2016 , 78N B:1122	BINDING SITE FOR RESIDUE 78N A1123
16	BC7	SOFTWARE	VAL A:50 , ASP A:51 , ALA A:52 , ARG A:55 , 78N A:1123 , ILE B:114 , TRP B:117 , 78N B:1122 , 78N B:1123	BINDING SITE FOR RESIDUE 78N A1124
17	BC8	SOFTWARE	ILE A:110 , TRP A:117 , ALA D:46 , TRP D:47 , ARG D:55	BINDING SITE FOR RESIDUE 78M A1125
18	BC9	SOFTWARE	CYS A:41 , PHE A:120 , HOH A:2015 , LEU C:102 , ILE C:105 , 78N C:1122 , 78N C:1123 , LEU D:39 , 78M D:1125	BINDING SITE FOR RESIDUE 78M A1126

(no "SS Bond" information available for 3ZE3)

(no "Cis Peptide Bond" information available for 3ZE3)

(no "SAP(SNP)/Variant" information available for 3ZE3)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAGK_PROKAR	PS01069	Prokaryotic diacylglycerol kinase signature.	KDGL_ECOLI	70-81	6	A:69-80 B:69-80 C:69-80 D:69-80 E:69-80 F:69-80

Biological Unit 1 (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	- - - D:69-80 E:69-80 F:69-80

Biological Unit 2 (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 3ZE3)

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:116
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:116
                                    16        26        36        46        56        66        76        86        96       106       116      
           KDGL_ECOLI     7 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3ze3 A   6 GFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    15        25        35        45        55        65        75        85        95       105       115

Chain B from PDB  Type:PROTEIN  Length:98
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:98
                                    34        44        54        64        74        84        94       104       114        
           KDGL_ECOLI    25 AWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 3ze3 B  24 AWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    33        43        53        63        73        83        93       103       113

Chain C from PDB  Type:PROTEIN  Length:90
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:90
                                    42        52        62        72        82        92       102       112       122
           KDGL_ECOLI    33 RQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3ze3 C  32 RQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    41        51        61        71        81        91       101       111       121

Chain D from PDB  Type:PROTEIN  Length:108
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:108
                                    24        34        44        54        64        74        84        94       104       114        
           KDGL_ECOLI    15 AGYSWKGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3ze3 D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113

Chain E from PDB  Type:PROTEIN  Length:83
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:86
                                    46        56        66        76        86        96       106       116      
           KDGL_ECOLI    37 VAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh..---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 3ze3 E  36 VAVLLCVVIAA---VDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    45|   |   55        65        75        85        95       105       115      
                                     46  50

Chain F from PDB  Type:PROTEIN  Length:88
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:88
                                    44        54        64        74        84        94       104       114        
           KDGL_ECOLI    35 EGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 3ze3 F  34 EGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    43        53        63        73        83        93       103       113

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 3ZE3)

(no "CATH Domain" information available for 3ZE3)

(no "Pfam Domain" information available for 3ZE3)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3ze3)

Biological Units
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	3ze3
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3ze4	CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - WILD-TYPE
3ze5	CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - DELTA4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File