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(-) Description

Title :  CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE (ZINC-INHIBITED FORM)
 
Authors :  D. A. Whittington, K. M. Rusche, H. Shin, C. A. Fierke, D. W. Christianso
Date :  21 Apr 03  (Deposition) - 10 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Alpha+Beta Fold, Hydrophobic Tunnel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Whittington, K. M. Rusche, H. Shin, C. A. Fierke, D. W. Christianson
Crystal Structure Of Lpxc, A Zinc-Dependent Deacetylase Essential For Endotoxin Biosynthesis
Proc. Natl. Acad. Sci. Usa V. 100 8146 2003
PubMed-ID: 12819349  |  Reference-DOI: 10.1073/PNAS.1432990100

(-) 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
    Fragment: SEQUENCE DATABASE RESIDUE 2-271
    Gene: LPXC OR ENVA OR AQ_1772
    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): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1MYR2Ligand/IonMYRISTIC ACID
2ZN7Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MYR1Ligand/IonMYRISTIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MYR1Ligand/IonMYRISTIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1MYR1Ligand/IonMYRISTIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , ZN A:502 , HOH A:602BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREGLU A:78 , HIS A:265 , ZN A:501 , MYR A:601 , HOH A:602BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREHIS A:58 , HIS A:200 , HOH A:603 , HOH A:604BINDING SITE FOR RESIDUE ZN A 503
4AC4SOFTWAREGLY A:2 , GLU A:126 , ILE B:27 , HIS B:29 , GLU B:95BINDING SITE FOR RESIDUE ZN A 504
5AC5SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , ZN B:506 , HOH B:603BINDING SITE FOR RESIDUE ZN B 505
6AC6SOFTWAREGLU B:78 , HIS B:265 , ZN B:505 , MYR B:602 , HOH B:603BINDING SITE FOR RESIDUE ZN B 506
7AC7SOFTWAREHIS B:58 , HIS B:200 , HOH B:604 , HOH B:605BINDING SITE FOR RESIDUE ZN B 507
8AC8SOFTWAREHIS A:58 , GLU A:78 , THR A:191 , ILE A:201 , GLY A:207 , HIS A:265 , ZN A:502 , HOH A:633 , HOH A:732BINDING SITE FOR RESIDUE MYR A 601
9AC9SOFTWAREHIS B:58 , SER B:59 , GLU B:78 , THR B:191 , ILE B:201 , GLY B:207 , HIS B:265 , ZN B:506 , HOH B:603 , HOH B:624 , HOH B:734BINDING SITE FOR RESIDUE MYR B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P42)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P42)

(-) Exons   (0, 0)

(no "Exon" information available for 1P42)

(-) 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 d1p42a1 A:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d1p42a2 A:128-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                 SCOP domains
               CATH domains 1p42A01 A:2-128 lpxc deacetylase, domain 1                                                                               1p42A02 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
                 1p42 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 d1p42b1 B:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d1p42b2 B:128-280 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                 SCOP domains
               CATH domains 1p42B01 B:2-128 lpxc deacetylase, domain 1                                                                               1p42B02 B:129-280 lpxc deacetylase, domain 2                                                                                                       CATH domains
           Pfam domains (1) LpxC-1p42B01 B:2-280                                                                                                                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) LpxC-1p42B02 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.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p42 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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  1p42
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  LPXC_AQUAE | O67648
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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_AQUAE | O67648: 1xxe 1yh8 1yhc 2go3 2go4 2ier 2ies 2j65 2jt2 2o3z 3p3c 3p76 4oze 4u3b 4u3d 5dro 5drp

(-) Related Entries Specified in the PDB File

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