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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INTEGRAL MEMBRANE KINASE - V2.3
 
Authors :  D. Li, C. Boland, M. Caffrey
Date :  09 May 14  (Deposition) - 23 Jul 14  (Release) - 26 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Transferase, Dgka, In Meso Crystallization, In Vitro Expression, Lipid Metabolism, Lipidic Mesophase, Lipidic Cubic Phase, Lcp, Membrane Protein, Microcrystal, 7. 8 Mag, Thermostable Mutant (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Boland, D. Li, S. T. A. Shah, S. Haberstock, V. Dotsch, F. Bernhard, M. Caffrey
Cell-Free Expression And In Meso Crystallisation Of An Integral Membrane Kinase For Structure Determination.
Cell. Mol. Life Sci. V. 71 4895 2014
PubMed-ID: 25012698  |  Reference-DOI: 10.1007/S00018-014-1655-7

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE
    Atcc: 29425
    Chains: A, B, C, D, E, F
    EC Number: 2.7.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B-DGKA-DELTA7
    Expression System Strain: A19
    Expression System Taxid: 562
    Expression System Vector: PET22B
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Other Details: CELL-FREE EXPRESSION
    Synonym: DAGK, DIGLYCERIDE KINASE, DGK

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 22)

Asymmetric/Biological Unit (5, 22)
No.NameCountTypeFull Name
178M7Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
278N11Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
3FLC2Ligand/IonCITRATE ANION
4NA1Ligand/IonSODIUM ION
5ZN1Ligand/IonZINC ION

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP D:107 , HOH D:2016 , HOH D:2017 , HOH D:2032BINDING SITE FOR RESIDUE NA D1122
02AC2SOFTWAREGLU D:28 , GLU D:76 , FLC D:1124 , ZN D:1126BINDING SITE FOR RESIDUE FLC D1123
03AC3SOFTWAREASP B:49 , GLU D:28 , ALA D:30 , GLU D:69 , GLU D:76 , FLC D:1123 , ZN D:1126 , 78N D:1128 , HOH D:2009BINDING SITE FOR RESIDUE FLC D1124
04AC4SOFTWARETRP A:25 , ILE A:26 , MET A:63 , 78M A:1123 , 78M A:1124 , HOH A:2008 , 78N C:1126BINDING SITE FOR RESIDUE 78M A1122
05AC5SOFTWARE78M A:1122 , HOH A:2003 , TRP C:47 , 78M C:1123 , 78N C:1126BINDING SITE FOR RESIDUE 78M A1123
06AC6SOFTWAREGLY B:35 , VAL B:36 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120BINDING SITE FOR RESIDUE 78M D1125
07AC7SOFTWAREALA A:46 , ARG A:55 , 78M A:1122 , ILE B:110 , ILE B:114 , 78N B:1121 , 78N B:1123BINDING SITE FOR RESIDUE 78M A1124
08AC8SOFTWARELEU A:48 , GLY A:121 , LEU C:102 , ILE C:105 , 78M C:1123 , 78N C:1124 , 78N C:1125BINDING SITE FOR RESIDUE 78M A1125
09AC9SOFTWARETRP A:47 , GLU C:34 , VAL C:65 , GLU C:69 , ALA C:108 , TRP C:112 , 78M C:1123 , 78N C:1126BINDING SITE FOR RESIDUE 78M C1122
10BC1SOFTWAREVAL A:43 , TRP A:47 , LEU A:48 , 78M A:1123 , 78M A:1125 , LEU C:40 , ILE C:44 , 78M C:1122 , 78N C:1126BINDING SITE FOR RESIDUE 78M C1123
11BC2SOFTWAREGLU D:28 , GLU D:76 , FLC D:1123 , FLC D:1124BINDING SITE FOR RESIDUE ZN D1126
12BC3SOFTWAREGLN A:33 , VAL A:62 , 78M A:1125 , TRP C:117 , 78N C:1125 , TRP D:25 , ARG D:32 , VAL D:36BINDING SITE FOR RESIDUE 78N C1124
13BC4SOFTWARE78M A:1125 , ALA B:46 , ALA B:52 , ARG B:55 , ILE C:114 , TRP C:117 , SER C:118 , 78N C:1124 , GLN D:33 , VAL D:36 , LEU D:39 , LEU D:40BINDING SITE FOR RESIDUE 78N C1125
14BC5SOFTWAREALA A:30 , PHE A:31 , GLU A:34 , GLU A:69 , VAL A:101 , LEU A:102 , ILE A:105 , 78N A:1126 , ARG D:22 , TRP D:25 , ILE D:26 , MET D:66BINDING SITE FOR RESIDUE 78N D1127
15BC6SOFTWARETRP B:47 , ASP B:49 , HOH B:2002 , ALA D:30 , GLN D:33 , GLU D:34 , LEU D:102 , ILE D:105 , VAL D:109 , FLC D:1124 , HOH D:2018BINDING SITE FOR RESIDUE 78N D1128
16BC7SOFTWAREILE A:10 , ALA A:13 , ALA A:14 , SER A:17 , 78M A:1124 , SER B:98 , VAL B:101 , LEU B:102 , 78N B:1123BINDING SITE FOR RESIDUE 78N B1121
17BC8SOFTWAREILE A:106 , VAL A:109 , ALA A:113 , ILE A:114 , TRP A:117 , LEU D:39 , 78N D:1127BINDING SITE FOR RESIDUE 78N A1126
18BC9SOFTWARETRP A:25 , LEU A:39 , LEU A:40 , 78M A:1122 , 78M A:1123 , CYS C:41 , TRP C:47 , TRP C:112 , 78M C:1122 , 78M C:1123BINDING SITE FOR RESIDUE 78N C1126
19CC1SOFTWARECYS E:41 , VAL E:62 , GLU E:69 , TRP E:112 , HOH E:2005BINDING SITE FOR RESIDUE 78N E1122
20CC2SOFTWAREGLU B:34 , ALA B:37 , GLU B:69 , ILE B:105 , TRP B:112BINDING SITE FOR RESIDUE 78N B1122
21CC3SOFTWARE78M A:1124 , VAL B:109 , ILE B:114 , TRP B:117 , 78N B:1121BINDING SITE FOR RESIDUE 78N B1123
22CC4SOFTWAREASP A:107 , ARG C:55 , MET C:63 , HOH C:2001BINDING SITE FOR RESIDUE 78N C1127

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4D2E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4D2E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D2E)

(-) PROSITE Motifs  (1, 6)

Asymmetric/Biological Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAGK_PROKARPS01069 Prokaryotic diacylglycerol kinase signature.KDGL_ECOLI70-81
 
 
 
 
 		  6A:69-80
B:69-80
C:69-80
D:69-80
E:69-80
F:69-80

(-) Exons   (0, 0)

(no "Exon" information available for 4D2E)

(-) 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: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 .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 4d2e 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
                                    33        43        53        63        73        83        93       103       113        
           KDGL_ECOLI    24 AAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHF 121
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------DAGK_PROKAR ---------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4d2e B  23 AAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    32        42        52        62        72        82        92       102       112        


Chain C from PDB  Type:PROTEIN  Length:93
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:93
                                    39        49        59        69        79        89        99       109       119   
           KDGL_ECOLI    30 AAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains --------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                 4d2e C  29 AAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    38        48        58        68        78        88        98       108       118   


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
                 4d2e D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113        


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

    Alignment length:103
                                    29        39        49        59        69        79        89        99       109       119   
           KDGL_ECOLI    20 KGLRAAWINEAAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHFG 122
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh-------------hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4d2e E  19 KGLRAAWI-------------LCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                   | -         - |      48        58        68        78        88        98       108       118   
                                  26            40                                                                                 


Chain F from PDB  Type:PROTEIN  Length:92
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:92
                                    39        49        59        69        79        89        99       109       119  
           KDGL_ECOLI    30 AAFRQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHF 121
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DAGK_PROKAR ---------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4d2e F  29 AAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    38        48        58        68        78        88        98       108       118
   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  (0, 0)

(no "SCOP Domain" information available for 4D2E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D2E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D2E)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological 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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        KDGL_ECOLI | P0ABN1: 2kdc 3ze3 3ze4 3ze5 4bpd 4brb 4brr 4cjz 4ck0 4up6 4uxw 4uxx 4uxz 4uyo 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4D2E)