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(-) Description

Title :  CRYSTAL STRUCTURE OF THE AQUIFEX AEOLICUS LPXC/LPC-009 COMPLEX
 
Authors :  C. -J Lee, P. Zhou
Date :  04 Oct 10  (Deposition) - 05 Jan 11  (Release) - 16 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipid A Biosynthesis, Lipid A Synthesis, Lpxc, Baab Sandwich, Hydrolase, Deacetylation, Antibiotic, Acyl Udp-Glcnac, Hydroxamate, Lpc-009 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Lee, X. Liang, X. Chen, D. Zeng, S. H. Joo, H. S. Chung, A. W. Barb, S. M. Swanson, R. A. Nicholas, Y. Li, E. J. Toone, C. R. Raetz, P. Zhou
Species-Specific And Inhibitor-Dependent Conformations Of Lpxc: Implications For Antibiotic Design.
Chem. Biol. V. 18 38 2011
PubMed-ID: 21167751  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.11.011

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-275
    Gene: AQ_1772, ENVA, LPXC
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: UDP-3-O-ACYL-GLCNAC DEACETYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
13P31Ligand/IonN-[(1S,2R)-2-HYDROXY-1-(HYDROXYCARBAMOYL)PROPYL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE
2PO41Ligand/IonPHOSPHATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:74 , HIS A:226 , ASP A:230 , 3P3 A:501BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREILE A:18 , HIS A:58 , GLU A:73 , HIS A:74 , GLU A:120 , THR A:179 , PHE A:180 , ILE A:189 , GLY A:198 , SER A:199 , HIS A:226 , LYS A:227 , ASP A:230 , HIS A:253 , ZN A:401 , HOH A:1292BINDING SITE FOR RESIDUE 3P3 A 501
3AC3SOFTWAREHIS A:29 , PHE A:40 , TYR A:45 , HOH A:1163BINDING SITE FOR RESIDUE PO4 A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P3C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P3C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P3C)

(-) Exons   (0, 0)

(no "Exon" information available for 3P3C)

(-) 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
(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:272
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:272
                                    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       261       271  
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQKLTRDL 273
               SCOP domains d3p3ca1 A:2-127 automated matches                                                                                             d3p3ca2 A:128-273 automated matches                                                                                                                SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains LpxC-3p3cA01 A:2-268                                                                                                                                                                                                                                                       ----- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p3c A   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQKLTRDL 273
                                    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       261       271
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P3C)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LPXC_AQUAE | O67648)
molecular function
    GO:0008759    UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity    Catalysis of the removal of an acetyl group from the 2-N position of glucosamine in the lipid A precursor UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine.
    GO:0103117    UDP-3-O-acyl-N-acetylglucosamine deacetylase activity    Catalysis of the reaction: UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetylglucosamine(2-) + H2O <=> UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine(1-) + acetate
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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  3p3c
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  LPXC_AQUAE | O67648
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  3.5.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_AQUAE | O67648: 1p42 1xxe 1yh8 1yhc 2go3 2go4 2ier 2ies 2j65 2jt2 2o3z 3p76 4oze 4u3b 4u3d 5dro 5drp

(-) Related Entries Specified in the PDB File

2jt2
3p3e CRYSTAL STRUCTURE OF THE PSEUDOMONAS AERUGINOSA LPXC/LPC- 009 COMPLEX
3p3g CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI LPXC/LPC-009 COMPLEX