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(-) Description

Title :  STRUCTURE OF DELTA7-DGKA-SYN IN 7.9 MAG TO 2.18 ANGSTROM RESOLUTION
 
Authors :  D. Li, N. Howe, M. Caffrey
Date :  27 Aug 14  (Deposition) - 30 Sep 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
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, Diacylglyerol Kinase, In Meso Crystallization, Lipid Cubic Phase, Lipidic Cubic Phase, Lipid Mesophase, Lipidic Mesophase, Membrane Protein, Monoacylglycerol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Li, P. J. Stansfeld, M. S. P. Sansom, A. Keogh, L. Vogeley, N. Howe, J. A. Lyons, D. Aragao, P. Fromme, R. Fromme, S. Basu, I. Grotjohann, C. Kupitz, K. Rendek, U. Weierstall, N. A. Zatsepin, V. Cherezov, W. Liu, S. Bandaru, N. J. English, C. Gati, A. Barty, O. Yefanov, H. N. Chapman, K. Diederichs, M. Messerschmidt, S. Boutet, G. J. Williams, M. Marvin Seibert, M. Caffrey
Ternary Structure Reveals Mechanism Of A Membrane Diacylglycerol Kinase.
Nat. Commun. V. 6 10140 2015
PubMed-ID: 26673816  |  Reference-DOI: 10.1038/NCOMMS10140

(-) Compounds

Molecule 1 - DIACYLGLYCEROL KINASE-DELTA 7
    Atcc: 29425
    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

 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  (5, 14)

Asymmetric Unit (5, 14)
No.NameCountTypeFull Name
179M7Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N4Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3ACT1Ligand/IonACETATE ION
4FLC1Ligand/IonCITRATE ANION
5ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
179M6Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N3Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3ACT-1Ligand/IonACETATE ION
4FLC-1Ligand/IonCITRATE ANION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
179M1Ligand/Ion(2R)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
279N1Ligand/Ion(2S)-2,3-DIHYDROXYPROPYL (7Z)-HEXADEC-7-ENOATE
3ACT1Ligand/IonACETATE ION
4FLC1Ligand/IonCITRATE ANION
5ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU D:28 , GLU D:76 , FLC D:1125 , ACT D:1126BINDING SITE FOR RESIDUE ZN D1122
02AC2SOFTWAREGLN A:33 , GLU A:34 , CYS A:41 , TRP C:117 , ARG D:32 , VAL D:36 , 79M D:1124BINDING SITE FOR RESIDUE 79M C1122
03AC3SOFTWAREVAL B:50 , ALA B:52 , ARG B:55 , ILE C:114 , GLN D:33BINDING SITE FOR RESIDUE 79M B1121
04AC4SOFTWAREILE B:26 , GLY B:35 , VAL B:38 , LEU D:40 , TRP D:47 , LEU D:48 , PHE D:120BINDING SITE FOR RESIDUE 79N D1123
05AC5SOFTWAREGLU B:34 , CYS B:41 , VAL B:62 , VAL B:65 , GLU B:69 , ALA B:108 , TRP B:112 , LEU B:116BINDING SITE FOR RESIDUE 79M B1122
06AC6SOFTWAREALA A:30 , PHE A:31 , GLU A:34 , GLU A:69 , LEU A:102 , 79M C:1122 , ARG D:22 , TRP D:25 , ILE D:26 , LEU D:39BINDING SITE FOR RESIDUE 79M D1124
07AC7SOFTWAREARG A:22 , TRP A:25 , MET A:63 , 79M A:1125 , ILE B:110BINDING SITE FOR RESIDUE 79N A1122
08AC8SOFTWAREASP B:49 , GLU D:34 , LEU D:102 , ILE D:105 , VAL D:109 , ALA D:113BINDING SITE FOR RESIDUE 79M B1123
09AC9SOFTWAREGLU D:28 , GLU D:76 , ZN D:1122 , ACT D:1126 , HOH D:2032 , HOH D:2033BINDING SITE FOR RESIDUE FLC D1125
10BC1SOFTWAREVAL A:43 , TRP A:47 , LEU A:48 , PHE A:120 , 79N A:1124 , LEU C:102 , ILE C:105BINDING SITE FOR RESIDUE 79N A1123
11BC2SOFTWARELEU A:40 , TRP A:47 , 79N A:1123 , GLU C:34BINDING SITE FOR RESIDUE 79N A1124
12BC3SOFTWAREGLU D:28 , GLU D:69 , ASN D:72 , SER D:73 , GLU D:76 , ZN D:1122 , FLC D:1125 , HOH D:2015BINDING SITE FOR RESIDUE ACT D1126
13BC4SOFTWAREARG A:55 , 79N A:1122 , 79M A:1126 , HOH A:2028BINDING SITE FOR RESIDUE 79M A1125
14BC5SOFTWAREALA A:52 , ARG A:55 , 79M A:1125 , ALA B:113 , ILE B:114 , TRP B:117 , SER B:118BINDING SITE FOR RESIDUE 79M A1126

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4UXZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4UXZ)

(-) 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:117
                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 4uxz A   5 TGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    14        24        34        44        54        64        74        84        94       104       114       


Chain B from PDB  Type:PROTEIN  Length:97
                                                                                                                                 
               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 ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 4uxz B  24 AWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    33        43        53        63        73        83        93       103       113       


Chain C from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               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 ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 4uxz C  32 RQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    41        51        61        71        81        91       101       111       121


Chain D from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               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 ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4uxz D  14 AGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    23        33        43        53        63        73        83        93       103       113        


Chain E from PDB  Type:PROTEIN  Length:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4uxz E  17 SWKGLRAAWIRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG 121
                                    26|       41        51        61        71        81        91       101       111       121
                                    26|                                                                                         
                                     32                                                                                         


Chain F from PDB  Type:PROTEIN  Length:95
                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 4uxz F  26 INEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHF 120
                                    35        45        55        65        75        85        95       105       115
   Legend:   → Mismatch (orange background)
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  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 4UXZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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  2.7.1.107
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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 4d2e 4up6 4uxw 4uxx 4uyo 5d56 5d57 5d6i 5dwk

(-) Related Entries Specified in the PDB File

4uxw STRUCTURE OF DELTA4-DGKA-APO IN 9.9 MAG
4uxx STRUCTURE OF DELTA4-DGKA WITH AMPPCP IN 9.9 MAG