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(-) Description

Title :  STRUCTURE OF A PHOSPHATIDYLINOSITOLPHOSPHATE (PIP) SYNTHASE FROM RENIBACTERIUM SALMONINARUM
 
Authors :  O. B. Clarke, D. T. Tomasek, C. D. Jorge, M. Belcher Dufrisne, M. Kim, S. K. R. Rajashankar, W. A. Hendrickson, H. Santos, F. Mancia
Date :  18 Aug 15  (Deposition) - 04 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.62
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Membrane Protein, Enzyme, Lipid Biosynthesis, Phosphatidylinositol (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. B. Clarke, D. Tomasek, C. D. Jorge, M. B. Dufrisne, M. Kim, S. Banerjee, K. R. Rajashankar, L. Shapiro, W. A. Hendrickson, H. Santos, F. Mancia
Structural Basis For Phosphatidylinositol-Phosphate Biosynthesis.
Nat Commun V. 6 8505 2015
PubMed-ID: 26510127  |  Reference-DOI: 10.1038/NCOMMS9505

(-) Compounds

Molecule 1 - AF2299 PROTEIN,PHOSPHATIDYLINOSITOL SYNTHASE
    Chains: D, A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: AF_2299, RSAL33209_2010
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS, RENIBACTERIUM SALMONINARUM
    Organism Taxid: 224325, 288705
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126, ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 45)

Asymmetric Unit (3, 45)
No.NameCountTypeFull Name
158A4Ligand/Ion5'-O-[(R)-{[(S)-{(2R)-2,3-BIS[(9E)-OCTADEC-9-ENOYLOXY]PROPOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]CYTIDINE
28K633Ligand/IonOCTADECANE
3MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
158A2Ligand/Ion5'-O-[(R)-{[(S)-{(2R)-2,3-BIS[(9E)-OCTADEC-9-ENOYLOXY]PROPOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]CYTIDINE
28K620Ligand/IonOCTADECANE
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
158A2Ligand/Ion5'-O-[(R)-{[(S)-{(2R)-2,3-BIS[(9E)-OCTADEC-9-ENOYLOXY]PROPOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]CYTIDINE
28K613Ligand/IonOCTADECANE
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU D:44binding site for residue 8K6 D 301
02AC2SOFTWAREPRO D:48binding site for residue 8K6 D 302
03AC3SOFTWARETHR D:114binding site for residue 8K6 D 303
04AC4SOFTWARESER D:27 , 8K6 D:307binding site for residue 8K6 D 304
05AC5SOFTWAREVAL D:61 , SER D:65 , 8K6 D:307binding site for residue 8K6 D 306
06AC6SOFTWAREVAL D:26 , 8K6 D:304 , 8K6 D:306binding site for residue 8K6 D 307
07AC7SOFTWAREASN D:3binding site for residue 8K6 D 309
08AC8SOFTWAREASP D:66 , ASP D:87 , ASP D:91 , MG D:314 , 58A D:315binding site for residue MG D 313
09AC9SOFTWAREASP D:66 , ASP D:69 , GLY D:70 , ASP D:87 , MG D:313 , 58A D:315binding site for residue MG D 314
10AD1SOFTWAREPRO D:28 , ASP D:29 , THR D:32 , THR D:60 , VAL D:63 , PHE D:64 , ASP D:66 , ILE D:67 , ASP D:69 , GLY D:70 , ALA D:73 , ARG D:74 , ARG D:78 , GLU D:79 , GLY D:80 , GLY D:83 , ALA D:84 , LEU D:86 , ASP D:87 , ARG D:150 , VAL D:155 , LEU D:166 , MG D:313 , MG D:314binding site for residue 58A D 315
11AD2SOFTWAREILE A:104binding site for residue 8K6 A 301
12AD3SOFTWARELEU A:44 , MET A:49binding site for residue 8K6 A 302
13AD4SOFTWAREILE A:121binding site for residue 8K6 A 303
14AD5SOFTWAREVAL A:61binding site for residue 8K6 A 304
15AD6SOFTWAREVAL A:26 , SER A:65binding site for residue 8K6 A 305
16AD7SOFTWAREVAL A:179binding site for residue 8K6 A 306
17AD8SOFTWARETRP A:171binding site for residue 8K6 A 307
18AD9SOFTWAREASP A:66 , ASP A:87 , ASP A:91 , MG A:310 , 58A A:311binding site for residue MG A 309
19AE1SOFTWAREASP A:66 , ASP A:69 , ASP A:87 , MG A:309 , 58A A:311binding site for residue MG A 310
20AE2SOFTWAREPRO A:28 , ASP A:29 , THR A:32 , THR A:56 , THR A:60 , VAL A:63 , PHE A:64 , ASP A:66 , ILE A:67 , ASP A:69 , GLY A:70 , ALA A:73 , ARG A:74 , GLU A:79 , GLY A:80 , GLY A:83 , ALA A:84 , ASP A:87 , ARG A:150 , SER A:151 , VAL A:155 , LEU A:166 , MG A:309 , MG A:310 , 58A B:309binding site for residue 58A A 311
21AE3SOFTWARESER B:65binding site for residue 8K6 B 301
22AE4SOFTWAREILE C:121binding site for residue 8K6 B 302
23AE5SOFTWAREPRO B:16binding site for residue 8K6 B 306
24AE6SOFTWAREASP B:66 , ASP B:87 , ASP B:91 , MG B:308 , 58A B:309binding site for residue MG B 307
25AE7SOFTWAREASP B:66 , ASP B:69 , GLY B:70 , ASP B:87 , MG B:307 , 58A B:309binding site for residue MG B 308
26AE8SOFTWARE58A A:311 , SER B:-1 , GLY B:0 , ASP B:29 , THR B:32 , PHE B:53 , THR B:60 , VAL B:63 , PHE B:64 , ASP B:66 , ILE B:67 , ASP B:69 , GLY B:70 , ALA B:73 , ARG B:74 , ARG B:78 , GLU B:79 , GLY B:83 , ALA B:84 , ASP B:87 , ARG B:150 , SER B:151 , VAL B:155 , MG B:307 , MG B:308binding site for residue 58A B 309
27AE9SOFTWARE8K6 C:302binding site for residue 8K6 C 301
28AF1SOFTWARETRP C:54 , 8K6 C:301binding site for residue 8K6 C 302
29AF2SOFTWARELEU C:44binding site for residue 8K6 C 304
30AF3SOFTWAREVAL C:26 , 8K6 C:307binding site for residue 8K6 C 306
31AF4SOFTWAREVAL C:34 , SER C:65 , 8K6 C:306binding site for residue 8K6 C 307
32AF5SOFTWAREASP C:66 , ASP C:87 , ASP C:91 , MG C:309 , 58A C:310binding site for residue MG C 308
33AF6SOFTWAREASP C:66 , ASP C:69 , GLY C:70 , ASP C:87 , MG C:308 , 58A C:310binding site for residue MG C 309
34AF7SOFTWAREPRO C:28 , ASP C:29 , THR C:32 , THR C:60 , VAL C:63 , PHE C:64 , ASP C:66 , ILE C:67 , ASP C:69 , GLY C:70 , ALA C:73 , ARG C:74 , GLU C:79 , GLY C:80 , GLY C:83 , ALA C:84 , ASP C:87 , ARG C:150 , SER C:151 , VAL C:155 , VAL C:159 , LEU C:166 , MG C:308 , MG C:309binding site for residue 58A C 310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D92)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:-2 -Ser A:-1

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D92)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D92)

(-) Exons   (0, 0)

(no "Exon" information available for 5D92)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhh.ee..eehhhhhhhhhhhh..eeeee.........eeeee...eee..........eeeee..eeeeeeehhhhhhh...hhhhhhhhhhhhh...eee..eee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d92 A -137 MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIGSGSKYARGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVIWFFLGGANPTIAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVATGLVGLGIPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWTA  204
                                  -128      -118      -108       -98       -88       -78       -68       -58       -48       -38       -28       -18        -8        |4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
                                                                                                                                                                      1|                                                                                                                                                                                                        
                                                                                                                                                                       4                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhh.ee..eehhhhhhhhhhhh..eeeee.........eeeee...eee..........eeeee..eeeeeeehhhhhhh...hhhhhhhhhhhhh...eee..eee....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5d92 B -137 MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIGSGSLNKYARGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVIWFFLGGANPTIAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVATGLVGLGIPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWTA  204
                                  -128      -118      -108       -98       -88       -78       -68       -58       -48       -38       -28       -18        -8         2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202  


Chain C from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee..eehhhhhhhhhhhh..eeeee..........eeee...eee..........eeeee..eeeeeeehhhhhhh...hhhhhhhhhhhhh...eee..eee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5d92 C -137 MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIGRGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVIWFFLGGANPTIAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVATGLVGLGIPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWTA  204
                                  -128      -118      -108       -98       -88       -78       -68       -58       -48       -38       -28       -18        -8     || 10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200    
                                                                                                                                                                  -2|                                                                                                                                                                                                     
                                                                                                                                                                    7                                                                                                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee..hhhh.ee..eehhhhhhhhhhhh..eeeee.........eeeee...eee..........eeeee..eeeeeeehhhhhhh...hhhhhhhhhhhhh...eee..eee....hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5d92 D -137 MRLAYVKNHEIYGEKLLGLTLRERIEKTLQRAGFDVRFFDELSLEEAEDYLIILEPVLILERDLLLEGRKILVSDGFTVGYFFGGDFRTVFDGNLQSSIEKYLSLNNLESYEIWAIKLSNDNLKTAEKLLLSSLIGSGSLNKYARGLFAAIFLPIARLLADWGVSPDAVTVVGTLGVMAGALIFYPMGQLFWGTVVITVFVFSDIIDGLMARLLFREGPWGAFLDSYLDRVGDSSVFTGIVIWFFLGGANPTIAILALICLVLSSLVSYSKARAEGLGLTANVGIAERSERLVVVLVATGLVGLGIPSWVLLVVLIVLAIASVVTIFQRVLTVREQAKAWTA  204
                                  -128      -118      -108       -98       -88       -78       -68       -58       -48       -38       -28       -18        -8         2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   Legend:   → Mismatch (orange background)
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  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 5D92)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D92)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D92)

(-) Gene Ontology  (7, 12)

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  5d92
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 Related Entries

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

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        A9WSF5_RENSM | A9WSF5: 5d91
        O27985_ARCFU | O27985: 4o6m 4o6n 4q7c 5d91

(-) Related Entries Specified in the PDB File

5d91 SAME PROTEIN, SLIGHTLY DIFFERENT CHIMERIC CONSTRUCT BOUNDARIES, IN APO STATE.