3GP6 - JenaLib

Title :   CRYSTAL STRUCTURE OF PAGP IN SDS/MPD

Authors :   J. A. Cuesta-Seijo, G. G. Prive

Date :   20 Mar 09 (Deposition) - 23 Jun 10 (Release) - 06 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Palmitoyltransferase, Beta-Barrel, Outer Membrane Enzyme, Pagp, Sds, Mpd, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. A. Cuesta-Seijo, C. Neale, M. A. Khan, J. Moktar, C. D. Tran, R. E. Bishop, R. Pomes, G. G. Prive
Pagp Crystallized From Sds/Cosolvent Reveals The Route For Phospholipid Access To The Hydrocarbon Ruler.
Structure V. 18 1210 2010
PubMed-ID: 20826347 | Reference-DOI: 10.1016/J.STR.2010.06.014

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 24)

Sites (24, 24)

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:10 , TYR A:70 , ILE A:84 , ARG A:114 , TRP A:156	BINDING SITE FOR RESIDUE SDS A 163
02	AC2	SOFTWARE	ALA A:14 , TRP A:17 , GLN A:18 , PHE A:55 , TYR A:70 , MPD A:174 , MPD A:177	BINDING SITE FOR RESIDUE SDS A 164
03	AC3	SOFTWARE	TRP A:93 , PRO A:95 , LEU A:105 , SER A:130	BINDING SITE FOR RESIDUE SDS A 165
04	AC4	SOFTWARE	ILE A:30 , PHE A:36 , TYR A:46 , PHE A:101 , VAL A:131 , GLY A:132 , TYR A:133 , PRO A:135 , PHE A:138	BINDING SITE FOR RESIDUE SDS A 166
05	AC5	SOFTWARE	TRP A:51 , LYS A:75 , TRP A:81 , SO4 A:180	BINDING SITE FOR RESIDUE SDS A 167
06	AC6	SOFTWARE	SER A:91 , LEU A:105 , GLY A:106 , SO4 A:179	BINDING SITE FOR RESIDUE SDS A 168
07	AC7	SOFTWARE	LEU A:105 , PRO A:127 , LEU A:128 , SO4 A:183 , HOH A:205 , HOH A:231	BINDING SITE FOR RESIDUE MPD A 169
08	AC8	SOFTWARE	ALA A:109 , PRO A:121 , LEU A:122 , PRO A:123 , MPD A:174	BINDING SITE FOR RESIDUE MPD A 170
09	AC9	SOFTWARE	PRO A:20 , GLU A:21 , HIS A:22 , LEU A:162 , SO4 A:184 , LI A:185	BINDING SITE FOR RESIDUE MPD A 171
10	BC1	SOFTWARE	TRP A:5 , PHE A:9 , HOH A:232	BINDING SITE FOR RESIDUE MPD A 172
11	BC2	SOFTWARE	GLY A:53 , ALA A:71 , MET A:72 , SO4 A:180 , HOH A:239	BINDING SITE FOR RESIDUE MPD A 173
12	BC3	SOFTWARE	ARG A:10 , ILE A:13 , TRP A:117 , LEU A:122 , SDS A:164 , MPD A:170	BINDING SITE FOR RESIDUE MPD A 174
13	BC4	SOFTWARE	ASP A:3 , ALA A:97 , ASP A:98 , TYR A:142	BINDING SITE FOR RESIDUE MPD A 175
14	BC5	SOFTWARE	ALA A:113 , PRO A:121	BINDING SITE FOR RESIDUE MPD A 176
15	BC6	SOFTWARE	ASN A:116 , TRP A:117 , ASN A:118 , SDS A:164	BINDING SITE FOR RESIDUE MPD A 177
16	BC7	SOFTWARE	PHE A:9 , ASN A:12 , TYR A:87 , TRP A:89 , PHE A:107	BINDING SITE FOR RESIDUE MRD A 178
17	BC8	SOFTWARE	PHE A:107 , LEU A:125 , LEU A:126 , SDS A:168 , SO4 A:183	BINDING SITE FOR RESIDUE SO4 A 179
18	BC9	SOFTWARE	GLY A:53 , ALA A:73 , TRP A:81 , SDS A:167 , MPD A:173	BINDING SITE FOR RESIDUE SO4 A 180
19	CC1	SOFTWARE	HOH A:233	BINDING SITE FOR RESIDUE SO4 A 181
20	CC2	SOFTWARE	TRP A:17 , LEU A:162 , SO4 A:184	BINDING SITE FOR RESIDUE SO4 A 182
21	CC3	SOFTWARE	ALA A:2 , PRO A:127 , TYR A:142 , MPD A:169 , SO4 A:179	BINDING SITE FOR RESIDUE SO4 A 183
22	CC4	SOFTWARE	TYR A:23 , MPD A:171 , SO4 A:182	BINDING SITE FOR RESIDUE SO4 A 184
23	CC5	SOFTWARE	PRO A:20 , GLU A:21 , HIS A:22 , LEU A:162 , MPD A:171	BINDING SITE FOR RESIDUE LI A 185
24	CC6	SOFTWARE	GLU A:21 , HIS A:22 , HOH A:200 , HOH A:201 , HOH A:215	BINDING SITE FOR RESIDUE LI A 186

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:155
 aligned with PAGP_ECOLI | P37001 from UniProtKB/Swiss-Prot  Length:186

    Alignment length:163
                                                                                                                                                                                           186 
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184 | 
           PAGP_ECOLI    25 ANADEWMTTFRENIAQTWQQPEHYDLYIPAITWHARFAYDKEKTDRYNERPWGGGFGLSRWDEKGNWHGLYAMAFKDSWNKWEPIAGYGWESTWRPLADENFHLGLGFTAGVTARDNWNYIPLPVLLPLASVGYGPVTFQMTYIPGTYNNGNVYFAWMRFQF-   -
               SCOP domains d3gp6a_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....--------......eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeeeee.......eeeeeeeeeeeee.hhhh..eeeeeeeeeeeee..eeeeeeee........eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gp6 A   0 MNADEWMTTFRENIAQTWQQPEHYDLYIPAITWHARFA--------YNERPWGGGFGLSRWDEKGNWHGLYAMAFKDSWNKWEPIAGYGWESTWRPLADENFHLGLGFTAGVTARDNWNYIPLPVLLPLASVGYGPVTFQMTYIPGTYNNGNVYFAWMRFQFL 162
                                     9        19        29       | -      | 49        59        69        79        89        99       109       119       129       139       149       159   
                                                                37       46

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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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PAGP_ECOLI | P37001)

molecular function
	GO:0016416	O-palmitoyltransferase activity	Catalysis of the transfer of a palmitoyl group to an oxygen atom on the acceptor molecule.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0009245	lipid A biosynthetic process	The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	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.

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