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(-) Description

Title :  STRUCTURE OF LPXC FROM YERSINIA ENTEROCOLITICA COMPLEXED WITH CHIR090 INHIBITOR
 
Authors :  K. E. Cole, D. W. Christianson
Date :  16 Jul 10  (Deposition) - 05 Jan 11  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Deacetylase, Endotoxin, Metal-Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Cole, S. G. Gattis, H. D. Angell, C. A. Fierke, D. W. Christianson
Structure Of The Metal-Dependent Deacetylase Lpxc From Yersinia Enterocolitica Complexed With The Potent Inhibitor Chir-090 .
Biochemistry V. 50 258 2010
PubMed-ID: 21171638  |  Reference-DOI: 10.1021/BI101622A

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B
    EC Number: 3.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PET11A
    Gene: LPXC, YE0678
    Organism Scientific: YERSINIA ENTEROCOLITICA
    Organism Taxid: 630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1C902Ligand/IonN-{(1S,2R)-2-HYDROXY-1-[(HYDROXYAMINO)CARBONYL]PROPYL}-4-{[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ETHYNYL}BENZAMIDE
2GOL1Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1C901Ligand/IonN-{(1S,2R)-2-HYDROXY-1-[(HYDROXYAMINO)CARBONYL]PROPYL}-4-{[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ETHYNYL}BENZAMIDE
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1C901Ligand/IonN-{(1S,2R)-2-HYDROXY-1-[(HYDROXYAMINO)CARBONYL]PROPYL}-4-{[4-(MORPHOLIN-4-YLMETHYL)PHENYL]ETHYNYL}BENZAMIDE
2GOL-1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:78 , HIS A:79 , THR A:191 , PHE A:192 , MET A:195 , ILE A:198 , GLN A:202 , CYS A:207 , GLY A:210 , SER A:211 , VAL A:217 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:307 , HOH A:366 , HOH A:390 , HOH A:400 , HOH A:454BINDING SITE FOR RESIDUE C90 A 501
2AC2SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , C90 A:501BINDING SITE FOR RESIDUE ZN A 307
3AC3SOFTWAREGLU A:134 , GLU A:280 , HOH A:451 , GLU B:69 , ASP B:220BINDING SITE FOR RESIDUE GOL A 3968
4AC4SOFTWAREGLU B:78 , HIS B:79 , THR B:191 , PHE B:192 , ILE B:198 , GLN B:202 , CYS B:207 , GLY B:210 , SER B:211 , PHE B:212 , VAL B:217 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:307 , HOH B:363 , HOH B:373BINDING SITE FOR RESIDUE C90 B 501
5AC5SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , C90 B:501BINDING SITE FOR RESIDUE ZN B 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:45 -Pro A:46
2Asn B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NZK)

(-) 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:298
 aligned with A1JJJ9_YERE8 | A1JJJ9 from UniProtKB/TrEMBL  Length:311

    Alignment length:298
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295        
         A1JJJ9_YERE8     6 MIKQRTLKRIVQATGVGLHTGKKVTLTMRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIIIEVNAPEVPIMDGSASPFVYLLLDAGIEELNSAKKFLRLKETVRVEDGDKWAELSPFNGFRLDFTIDFNHPAIDSSTQRYRLDFSADSFVRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEFVTFQDEAEMPLAFK 303
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeee.......eeeee......eeee.hhhhh........ee.....ee..hhhhhhhhhhhh...eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee.hhhhhhhhh.....eeehhhhhhhhh............eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzk A   1 MIKQRTLKRIVQATGVGLHTGKKVTLTMRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIIIEVNAPEVPIMDGSASPFVYLLLDAGIEELNSAKKFLRLKETVRVEDGDKWAELSPFNGFRLDFTIDFNHPAIDSSTQRYRLDFSADSFVRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEFVTFQDEAEMPLAFK 298
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290        


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with A1JJJ9_YERE8 | A1JJJ9 from UniProtKB/TrEMBL  Length:311

    Alignment length:300
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305
         A1JJJ9_YERE8     6 MIKQRTLKRIVQATGVGLHTGKKVTLTMRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIIIEVNAPEVPIMDGSASPFVYLLLDAGIEELNSAKKFLRLKETVRVEDGDKWAELSPFNGFRLDFTIDFNHPAIDSSTQRYRLDFSADSFVRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEFVTFQDEAEMPLAFKAP 305
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -LpxC-3nzkB01 B:2-280                                                                                                                                                                                                                                                                   -------------------- Pfam domains (1)
           Pfam domains (2) -LpxC-3nzkB02 B:2-280                                                                                                                                                                                                                                                                   -------------------- Pfam domains (2)
         Sec.struct. author ..eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhhhh........ee.....ee..hhhhhhhhhhhh...eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee........hhhh.eeeee.hhhhhhhhh.....eeehhhhhhhhh............eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhh.eeee...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nzk B   1 MIKQRTLKRIVQATGVGLHTGKKVTLTMRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIIIEVNAPEVPIMDGSASPFVYLLLDAGIEELNSAKKFLRLKETVRVEDGDKWAELSPFNGFRLDFTIDFNHPAIDSSTQRYRLDFSADSFVRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEFVTFQDEAEMPLAFKAP 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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  (0, 0)

(no "SCOP Domain" information available for 3NZK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: S5 (103)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A1JJJ9_YERE8 | A1JJJ9)
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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