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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITH PYROPHOSPHATE
 
Authors :  H. A. Gennadios, D. W. Christianson
Date :  19 Sep 06  (Deposition) - 09 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha + Beta Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. A. Gennadios, D. W. Christianson
Binding Of Uridine 5-Diphosphate In The Basic Patch Of The Zinc Metalloenzyme Deacetylase Lpxc And Implications For Substrate Binding
Biochemistry V. 45 15216 2006
PubMed-ID: 17176043  |  Reference-DOI: 10.1021/BI0619021
(for further references see the PDB file header)

(-) 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 Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPXC
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: UDP-3-O-ACYL-GLCNAC DEACETYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2PLM2Ligand/IonPALMITIC ACID
3POP2Ligand/IonPYROPHOSPHATE 2-
4ZN5Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECL A:608 , HIS B:58 , POP B:700 , PLM B:802BINDING SITE FOR RESIDUE ZN A 602
02AC2SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , PLM A:801BINDING SITE FOR RESIDUE ZN A 603
03AC3SOFTWAREASN A:57 , HIS A:58 , LYS A:239 , HIS A:265 , ZN A:604BINDING SITE FOR RESIDUE POP A 701
04AC4SOFTWAREHIS A:58 , CL A:607 , POP A:701 , PLM A:801BINDING SITE FOR RESIDUE ZN A 604
05AC5SOFTWAREVAL A:254 , LYS A:255 , HOH A:814BINDING SITE FOR RESIDUE ZN A 606
06AC6SOFTWAREHIS A:58 , GLU A:78 , HIS A:79 , THR A:191 , ILE A:198 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:603 , ZN A:604 , CL A:607BINDING SITE FOR RESIDUE PLM A 801
07AC7SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , PLM B:802BINDING SITE FOR RESIDUE ZN A 605
08AC8SOFTWAREPHE A:192 , GLU A:197 , ZN A:604 , PLM A:801BINDING SITE FOR RESIDUE CL A 607
09AC9SOFTWAREZN A:602 , ASN B:57 , HIS B:58 , LYS B:239 , HIS B:265 , PLM B:802 , HOH B:806 , HOH B:807BINDING SITE FOR RESIDUE POP B 700
10BC1SOFTWAREZN A:602 , ZN A:605 , CL A:608 , HIS B:58 , GLU B:78 , HIS B:79 , THR B:191 , ILE B:198 , ILE B:201 , GLY B:210 , SER B:211 , LEU B:212 , HIS B:238 , ASP B:242 , HIS B:265 , POP B:700BINDING SITE FOR RESIDUE PLM B 802
11BC2SOFTWAREZN A:602 , GLU B:197 , PLM B:802BINDING SITE FOR RESIDUE CL A 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IES)

(-) 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: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 d2iesa1 A:2-133 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                             d2iesa2 A:134-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                           SCOP domains
               CATH domains 2iesA01 A:2-128 lpxc deacetylase, domain 1                                                                               2iesA02 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..........hhhhhhhhhhheeeeeee...ee....eeeee..eeeeeee....eeeeeee......eeeeeee..hhhhh....eeee..hhhhhhhh..........eeee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ies 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 d2iesb1 B:2-133 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                             d2iesb2 B:134-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                           SCOP domains
               CATH domains 2iesB01 B:2-128 lpxc deacetylase, domain 1                                                                               2iesB02 B: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..........hhhhhhhhhhheeeeeee...ee....eeeee..eeeeeee....eeeeeee......eeeeeee..hhhhh....eeee...hhhhhhh..........eeee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ies 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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IES)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological 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 2j65 2jt2 2o3z 3p3c 3p76 4oze 4u3b 4u3d 5dro 5drp

(-) Related Entries Specified in the PDB File

1p42 ZINC-INHIBITED CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC
1yh8 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH PALMITATE
1yhc CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH CACODYLATE
2go3 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITH IMIDAZOLE.
2go4 CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITH TU-514
2ier CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITH URIDINE 5'-DIPHOSPHATE