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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF LPXC COMPLEXED WITH 3-HEPTYLOXYBENZOATE
 
Authors :  H. A. Gennadios, D. A. Whittington, D. W. Christianson
Date :  02 Dec 06  (Deposition) - 27 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Keywords :  Lipid A Biosynthesis, Lipid Synthesis, Lpxc, 3-Heptyloxybenzoate, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Shin, H. A. Gennadios, D. A. Whittington, D. W. Christianson
Amphipathic Benzoic Acid Derivatives: Synthesis And Binding In The Hydrophobic Tunnel Of The Zinc Deacetylase Lpxc.
Bioorg. Med. Chem. V. 15 2617 2007
PubMed-ID: 17296300  |  Reference-DOI: 10.1016/J.BMC.2007.01.044

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPXC, ENVA
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: UDP-3-O-ACYL-GLCNAC DEACETYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)
Biological Unit 3 (1x): A 
Biological Unit 4 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1AI72Ligand/Ion3-(HEPTYLOXY)BENZOIC ACID
2CL1Ligand/IonCHLORIDE ION
3SO42Ligand/IonSULFATE ION
4ZN5Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AI72Ligand/Ion3-(HEPTYLOXY)BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1AI71Ligand/Ion3-(HEPTYLOXY)BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1AI71Ligand/Ion3-(HEPTYLOXY)BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1AI71Ligand/Ion3-(HEPTYLOXY)BENZOIC ACID
2CL-1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:56 , HIS A:58 , LYS A:239 , GLY A:264 , HIS A:265 , HOH A:622 , HOH A:668BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWARETHR B:56 , HIS B:58 , LYS B:239 , GLY B:264 , HIS B:265 , AI7 B:301BINDING SITE FOR RESIDUE SO4 B 401
03AC3SOFTWAREHIS A:79 , HIS A:238 , ASP A:242BINDING SITE FOR RESIDUE ZN A 501
04AC4SOFTWAREHIS A:58 , HIS A:200 , CL A:601 , HOH A:602BINDING SITE FOR RESIDUE ZN A 502
05AC5SOFTWAREHIS B:79 , HIS B:238 , ASP B:242BINDING SITE FOR RESIDUE ZN B 503
06AC6SOFTWAREHIS B:58 , HIS B:200 , HOH B:507 , HOH B:508BINDING SITE FOR RESIDUE ZN B 504
07AC7SOFTWAREGLY A:2 , GLU A:126 , HIS B:29 , GLU B:95BINDING SITE FOR RESIDUE ZN B 506
08AC8SOFTWAREPHE A:167 , HIS A:200 , ZN A:502BINDING SITE FOR RESIDUE CL A 601
09AC9SOFTWAREILE A:18 , ILE A:198 , LYS A:202 , GLY A:210 , SER A:211 , HOH A:667 , HOH A:699 , SER B:211 , LEU B:212 , AI7 B:301BINDING SITE FOR RESIDUE AI7 A 301
10BC1SOFTWARELEU A:212 , AI7 A:301 , ILE B:18 , ILE B:198 , ILE B:201 , LYS B:202 , GLY B:207 , GLY B:210 , SER B:211 , VAL B:217 , SO4 B:401BINDING SITE FOR RESIDUE AI7 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O3Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O3Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 2O3Z)

(-) 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:267
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:267
                                    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       
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
               SCOP domains d2o3za1 A:2-133 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                             d2o3za2 A:134-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                           SCOP domains
               CATH domains 2o3zA01 A:2-128 lpxc deacetylase, domain 1                                                                               2o3zA02 A:129-280 lpxc deacetylase, domain 2                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o3z A   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 280
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273       
                                                                                        63|                                              118|                                        163|     175|                                                                                                     
                                                                                         69                                               120                                         167      179                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:267
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:267
                                    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       
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
               SCOP domains d2o3zb1 B:2-133 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                             d2o3zb2 B:134-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                           SCOP domains
               CATH domains 2o3zB01 B:2-128 lpxc deacetylase, domain 1                                                                               2o3zB02 B:129-280 lpxc deacetylase, domain 2                                                                                                       CATH domains
           Pfam domains (1) LpxC-2o3zB01 B:2-280                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) LpxC-2o3zB02 B:2-280                                                                                                                                                                                                                                                        Pfam domains (2)
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o3z B   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 280
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273       
                                                                                        63|                                              118|                                        163|     175|                                                                                                     
                                                                                         69                                               120                                         167      179
   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, 4)

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

(-) CATH Domains  (2, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: S5 (103)
(-)
Family: LpxC (10)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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 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 3p3c 3p76 4oze 4u3b 4u3d 5dro 5drp

(-) Related Entries Specified in the PDB File

1p42 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE (ZINC-INHIBITED FORM)