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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE DIACYLGLYCEROL KINASE - DELTA 7.79
 
Authors :  D. Li, N. Howe, M. Caffrey
Date :  05 Jun 13  (Deposition) - 18 Jun 14  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.44
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Transferase, Dgka, In Meso Crystallization, Low Temperature Crystallization, Membrane Protein, Lcp, Lipidic Cubic Phase, Lipid Mesophase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Li, N. Howe, M. Caffrey
Crystal Structure Of An Integral Membrane Enzyme Determined By X-Ray Free Electron Laser Femtocrystallography
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE
    Atcc29425
    ChainsA, B, C, D, E, F
    EC Number2.7.1.107
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPTRCHISB-DGKA-DELTA 7
    Expression System StrainWH1061
    Expression System Taxid562
    Expression System VectorPTRCHISB
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificESCHERICHIA COLI K-12
    Organism Taxid83333
    SynonymDAGK, DIGLYCERIDE KINASE, DGK

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)ABC   
Biological Unit 2 (1x)   DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
179M3Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
2ACT1Ligand/IonACETATE ION
3FLC1Ligand/IonCITRATE ANION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
179M2Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
2ACT-1Ligand/IonACETATE ION
3FLC-1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
179M1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
2ACT1Ligand/IonACETATE ION
3FLC1Ligand/IonCITRATE ANION
4ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU D:28 , GLU D:76 , ACT D:1123 , FLC D:1124BINDING SITE FOR RESIDUE ZN D1122
2AC2SOFTWAREGLU D:28 , ALA D:30 , ASN D:72 , GLU D:76 , ZN D:1122BINDING SITE FOR RESIDUE ACT D1123
3AC3SOFTWAREGLU D:28 , GLU D:76 , ZN D:1122 , HOH D:2002 , HOH D:2003BINDING SITE FOR RESIDUE FLC D1124
4AC4SOFTWARETRP A:117 , ILE B:26 , GLY B:35 , MET B:63 , TRP D:47 , LEU D:48 , ASP D:49 , PHE D:120BINDING SITE FOR RESIDUE 79M D1125
5AC5SOFTWAREGLN A:33 , ALA A:37 , CYS A:41 , VAL A:109 , TRP A:112 , 79M B:1121 , TRP C:117 , TRP D:25 , ARG D:32 , GLN D:33 , VAL D:36BINDING SITE FOR RESIDUE 79M C1122
6AC6SOFTWAREALA B:52 , ARG B:55 , ILE C:110 , ILE C:114 , 79M C:1122 , GLN D:33 , VAL D:36 , LEU D:40BINDING SITE FOR RESIDUE 79M B1121

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric 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
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAGK_PROKARPS01069 Prokaryotic diacylglycerol kinase signature.KDGL_ECOLI70-81
 
 
 
 
 
  3A:69-80
B:69-80
C:69-80
-
-
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DAGK_PROKARPS01069 Prokaryotic diacylglycerol kinase signature.KDGL_ECOLI70-81
 
 
 
 
 
  3-
-
-
D:69-80
E:69-80
F:69-80

(-) Exons   (0, 0)

(no "Exon" information available for 4BRR)

(-) Sequences/Alignments

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
                 4brr 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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------DAGK_PROKAR ---------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4brr B  23 AAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    32        42        52        62        72        82        92       102       112        

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 .hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------DAGK_PROKAR ----------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4brr 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
                 4brr D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113        

Chain E from PDB  Type:PROTEIN  Length:87
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:87
                                    44        54        64        74        84        94       104       114       
           KDGL_ECOLI    35 EGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHF 121
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------DAGK_PROKAR ---------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 4brr E  34 EGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    43        53        63        73        83        93       103       113       

Chain F from PDB  Type:PROTEIN  Length:89
 aligned with KDGL_ECOLI | P0ABN1 from UniProtKB/Swiss-Prot  Length:122

    Alignment length:89
                                    42        52        62        72        82        92       102       112         
           KDGL_ECOLI    33 RQEGVAVLLAVVIACWLDVDAITRVLLISSVMLVMIVEILNSAIEAVVDRIGSEYHELSGRAKDMGSAAVLIAIIVAVITWCILLWSHF 121
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DAGK_PROKAR ---------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4brr F  32 RQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    41        51        61        71        81        91       101       111         

   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 4BRR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KDGL_ECOLI | P0ABN12kdc 3ze3 3ze4 3ze5 4bpd 4brb 4cjz 4ck0 4d2e 4up6 4uxw 4uxx 4uxz 4uyo 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

4brb CRYSTAL STRUCTURE OF THE INTEGRAL MEMBRANE ENZYME DGKA- REF, DELTA 7