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(-) Description

Title :  CRYSTAL STRUCTURE OF MEMBRANE ASSOCIATED PATA FROM MYCOBACTERIUM SMEGMATIS IN COMPLEX WITH S-HEXADECYL COENZYME A - P21 SPACE GROUP
 
Authors :  D. Albesa-Jove, Z. Svetlikova, A. Carreras-Gonzalez, M. Tersa, E. San Vaello, J. O. Cifuente, K. Mikusova, M. E. Guerin
Date :  02 Dec 15  (Deposition) - 09 Mar 16  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Acyltransferase, Glycolipid Biosynthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Albesa-Jove, Z. Svetlikova, M. Tersa, E. Sancho-Vaello, A. Carreras-Gonzalez, P. Bonnet, P. Arrasate, A. Eguskiza, S. K. Angala, J. O. Cifuente, J. Kordulakova, M. Jackson, K. Mikusova, M. E. Guerin
Structural Basis For Selective Recognition Of Acyl Chains B The Membrane-Associated Acyltransferase Pata.
Nat Commun V. 7 10906 2016
PubMed-ID: 26965057  |  Reference-DOI: 10.1038/NCOMMS10906

(-) Compounds

Molecule 1 - PHOSPHATIDYLINOSITOL MANNOSIDE ACYLTRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Expression System Taxid: 246196
    Expression System Vector Type: PLASMID
    Gene: MSMEG_2934, MSMEI_2860
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Synonym: PIM ACYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HD64Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(3~{S})-4-[[3-(2-HEXADECYLSULFANYLETHYLAMINO)-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] HYDROGEN PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HD61Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(3~{S})-4-[[3-(2-HEXADECYLSULFANYLETHYLAMINO)-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] HYDROGEN PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HD61Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(3~{S})-4-[[3-(2-HEXADECYLSULFANYLETHYLAMINO)-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] HYDROGEN PHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HD61Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(3~{S})-4-[[3-(2-HEXADECYLSULFANYLETHYLAMINO)-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] HYDROGEN PHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HD61Ligand/Ion[[(2~{R},3~{S},4~{R},5~{R})-5-(6-AMINOPURIN-9-YL)-4-OXIDANYL-3-PHOSPHONOOXY-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] [(3~{S})-4-[[3-(2-HEXADECYLSULFANYLETHYLAMINO)-3-OXIDANYLIDENE-PROPYL]AMINO]-2,2-DIMETHYL-3-OXIDANYL-4-OXIDANYLIDENE-BUTYL] HYDROGEN PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:122 , LEU A:124 , TRP A:130 , THR A:146 , VAL A:147 , ARG A:164 , PHE A:182 , CYS A:196 , MET A:198 , SER A:206 , PRO A:220 , GLY A:222 , GLU A:229binding site for residue HD6 A 401
2AC2SOFTWARETRP B:130 , ALA B:133 , GLY B:134 , THR B:146 , VAL B:147 , GLU B:149 , ARG B:164 , CYS B:196 , MET B:198 , PRO B:220 , GLY B:222binding site for residue HD6 B 401
3AC3SOFTWARELEU C:124 , TRP C:130 , ALA C:133 , GLY C:134 , CYS C:196 , MET C:198 , ASP C:202 , PRO C:220 , GLY C:222binding site for residue HD6 C 401
4AC4SOFTWARETRP D:130 , THR D:146 , VAL D:147 , GLU D:149 , ARG D:164 , PHE D:182 , CYS D:196 , MET D:198 , ARG D:201 , ASP D:202 , PRO D:220 , GLY D:222binding site for residue HD6 D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F34)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Lys A:152 -Pro A:153
2Lys B:152 -Pro B:153
3Lys C:152 -Pro C:153
4Lys D:152 -Pro D:153

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F34)

(-) Exons   (0, 0)

(no "Exon" information available for 5F34)

(-) 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:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee.........eeeee..eeeee.hhhhhhhhhhh.eeeeeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f34 A  50 PEQLRRNLARVVGKPPADVPDDLIRASLASYARYWREAFRLPAMDHGRLGEQLDVIDIDHLWSALDAGRGAVLALPHSGNWDMAGVWLVQNYGPFTTVAERLKPESLYRRFVEYRESLGFEVLPLTGGERPPFEVLAERLTDNRPICLMAERDLTRSGVQVDFFGEATRMPAGPAKLAIETGAALFPVHCWFEGDGWGMRVYPELDTSSGDVTAITQALADRFAANIATYPADWHMLQPQWIADLSDERRARL 302
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee.........eeeee..eeeee.hhhhhhhhhhh.eeeeeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f34 B  50 PEQLRRNLARVVGKPPADVPDDLIRASLASYARYWREAFRLPAMDHGRLGEQLDVIDIDHLWSALDAGRGAVLALPHSGNWDMAGVWLVQNYGPFTTVAERLKPESLYRRFVEYRESLGFEVLPLTGGERPPFEVLAERLTDNRPICLMAERDLTRSGVQVDFFGEATRMPAGPAKLAIETGAALFPVHCWFEGDGWGMRVYPELDTSSGDVTAITQALADRFAANIATYPADWHMLQPQWIADLSDERRARL 302
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299   


Chain C from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhh..eeee......hhhhhhhhhhhh..eeeee.........eeeee..eeeee.hhhhhhhhhhh.eeeeeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f34 C  50 PEQLRRNLARVVGKPPADVPDDLIRASLASYARYWREAFRLPAMDHGRLGEQLDVIDIDHLWSALDAGRGAVLALPHSGNWDMAGVWLVQNYGPFTTVAERLKPESLYRRFVEYRESLGFEVLPLTGGERPPFEVLAERLTDNRPICLMAERDLTRSGVQVDFFGEATRMPAGPAKLAIETGAALFPVHCWFEGDGWGMRVYPELDTSSGDVTAITQALADRFAANIATYPADWHMLQPQWIADLSDERRAR 301
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299  


Chain D from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh...eeeee....hhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh..eeeee.........eeeee..eeeee.hhhhhhhhhhh.eeeeeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f34 D  50 PEQLRRNLARVVGKPPADVPDDLIRASLASYARYWREAFRLPAMDHGRLGEQLDVIDIDHLWSALDAGRGAVLALPHSGNWDMAGVWLVQNYGPFTTVAERLKPESLYRRFVEYRESLGFEVLPLTGGERPPFEVLAERLTDNRPICLMAERDLTRSGVQVDFFGEATRMPAGPAKLAIETGAALFPVHCWFEGDGWGMRVYPELDTSSGDVTAITQALADRFAANIATYPADWHMLQPQWIADLSDERRARL 302
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299
   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 5F34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F34)

(-) Gene Ontology  (10, 10)

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  5f34
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 Related Entries

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        ACYLT_MYCS2 | A0QWG5: 5f2t 5f2z 5f31

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