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(-) Description

Title :  STRUCTURE OF PSEUDOMONAS AERUGINOSA LPXA IN COMPLEX WITH UDP-3-O-(R-3-HYDROXYDECANOYL)-GLCNAC
 
Authors :  E. W. Smith, Y. Chen
Date :  27 Aug 15  (Deposition) - 16 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D (1x),E (1x),F (1x)
Keywords :  Acyltransferases, Catalytic Domain, Udp-Glcnac, Fatty Acids, Lipid A, Substrate Specificity, Uridine Diphosphate N-Acetylglucosamine, Hydrocarbon Rulers, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Smith, X. Zhang, C. Behzadi, L. D. Andrews, F. Cohen, Y. Chen
Structures Of Pseudomonas Aeruginosa Lpxa Reveal The Basis For Its Substrate Selectivity.
Biochemistry V. 54 5937 2015
PubMed-ID: 26352800  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00720

(-) Compounds

Molecule 1 - ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N-ACETYLGLUCOSAMINE O- ACYLTRANSFERASE
    Chains: A, B, C, D, E, F
    EC Number: 2.3.1.129
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LPXA, PSPA7_1495
    Organism Scientific: PSEUDOMONAS AERUGINOSA (STRAIN PA7)
    Organism Taxid: 381754
    Strain: PA7
    Synonym: UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    D (1x)E (1x)F (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1PO41Ligand/IonPHOSPHATE ION
2U214Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
2U212Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1PO4-1Ligand/IonPHOSPHATE ION
2U211Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYDECANOYL)-N-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:114 , VAL A:132 , ASN A:133 , GLY A:151 , PHE A:166 , ASN A:194 , GLU A:196 , GLY A:197 , ARG A:200 , HOH A:309 , ASP B:70 , LEU B:71 , LYS B:72 , HIS B:118 , HIS B:121 , ALA B:136 , ALA B:138 , HIS B:140 , VAL B:155 , HIS B:156 , GLN B:157 , TYR B:158 , HOH B:414 , HOH B:415 , HOH B:428binding site for residue U21 B 301
2AC2SOFTWAREASN B:133 , ILE B:148 , PHE B:166 , ASN B:194 , GLU B:196 , ARG B:200 , PRO C:69 , ASP C:70 , LEU C:71 , LYS C:72 , HIS C:118 , HIS C:121 , ALA C:136 , ALA C:138 , HIS C:140 , VAL C:155 , GLN C:157 , HOH C:401binding site for residue U21 C 301
3AC3SOFTWAREMET D:114 , VAL D:132 , ASN D:133 , ILE D:148 , PHE D:166 , ASN D:194 , GLU D:196 , ARG D:200 , ARG D:201 , HOH D:403 , HOH D:410 , HOH D:411 , HOH D:419 , HOH D:422 , HOH D:433 , ASP F:70 , LEU F:71 , LYS F:72 , HIS F:118 , HIS F:121 , ALA F:136 , ALA F:138 , HIS F:140 , GLN F:157 , HOH F:310binding site for residue U21 D 301
4AC4SOFTWAREASP E:70 , LEU E:71 , LYS E:72 , HIS E:118 , HIS E:121 , ALA E:136 , ALA E:138 , HIS E:140 , GLN E:157 , HOH E:405 , MET F:114 , ASN F:133 , ILE F:148 , PHE F:166 , ASN F:194 , GLU F:196 , ARG F:200binding site for residue U21 E 301
5AC5SOFTWAREASN E:194 , GLU E:196 , ARG E:200binding site for residue PO4 E 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DG3)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:48 -Pro A:49
2Asn A:186 -Pro A:187
3Gly B:48 -Pro B:49
4Asn B:186 -Pro B:187
5Gly C:48 -Pro C:49
6Asn C:186 -Pro C:187
7Gly D:48 -Pro D:49
8Asn D:186 -Pro D:187
9Gly E:48 -Pro E:49
10Asn E:186 -Pro E:187
11Gly F:48 -Pro F:49
12Asn F:186 -Pro F:187

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DG3)

(-) Exons   (0, 0)

(no "Exon" information available for 5DG3)

(-) 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:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 A   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 B   2 SLIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 C   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      


Chain D from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee.....eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 D   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62      ||79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249         
                                                                                             69|                                                                                                                                                                                     
                                                                                              77                                                                                                                                                                                     


Chain E from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 E   3 LIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252      


Chain F from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......ee....ee....ee....ee...eee....ee....ee...eee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dg3 F   2 SLIDPRAIIDPSARLAADVQVGPWSIVGAEVEIGEGTVIGPHVVLKGPTKIGKHNRIYQFSSVGEDTPDLKYKGEPTRLVIGDHNVIREGVTIHRGTVQDRAETTIGDHNLIMAYAHIGHDSVIGNHCILVNNTALAGHVHVDDWAILSGYTLVHQYCRIGAHSFSGMGSAIGKDVPAYVTVFGNPAEARSMNFEGMRRRGFSSEAIHALRRAYKVVYRQGHTVEEALAELAESAAQFPEVAVFRDSIQSATRGITR 258
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 5DG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DG3)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXA_PSEA7 | A6V1E4: 5dem 5dep

(-) Related Entries Specified in the PDB File

5dem 5dep