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(-) Description

Title :  STRUCTURE OF LPXC BOUND TO THE REACTION PRODUCT UDP-(3-O-(R-3-HYDROXYMYRISTOYL))-GLUCOSAMINE
 
Authors :  G. M. Clayton, D. J. Klein, K. W. Rickert, S. B. Patel, M. Kornienko, J. Zu Murphy, J. C. Reid, S. Tummala, S. Sharma, S. B. Singh, L. Miesel, K. J. L S. M. Soisson
Date :  23 Aug 13  (Deposition) - 16 Oct 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Clayton, D. J. Klein, K. W. Rickert, S. B. Patel, M. Kornienko, J. Zugay-Murphy, J. C. Reid, S. Tummala, S. Sharma, S. B. Singh, L. Miesel, K. J. Lumb, S. M. Soisson
Structure Of The Bacterial Deacetylase Lpxc Bound To The Nucleotide Reaction Product Reveals Mechanisms Of Oxyanion Stabilization And Proton Transfer.
J. Biol. Chem. V. 288 34073 2013
PubMed-ID: 24108127  |  Reference-DOI: 10.1074/JBC.M113.513028

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
    Chains: A, B, C, D
    EC Number: 3.5.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LPXC, O3O_04310
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: LPXC, UDP-3-O-ACYL-GLCNAC DEACETYLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
124G4Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)-GLUCOSAMINE
2PO44Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
124G1Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
124G1Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
124G1Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
124G1Ligand/IonURIDINE-5'-DIPHOSPHATE-3-O-(R-3-HYDROXYMYRISTOYL)-GLUCOSAMINE
2PO41Ligand/IonPHOSPHATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:79 , HIS A:238 , ASP A:242 , PO4 A:403BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWARELEU A:62 , LYS A:143 , ILE A:159 , ASP A:160 , PHE A:161 , PHE A:192 , GLY A:210 , SER A:211 , VAL A:217 , LYS A:239 , LYS A:262 , GLY A:264 , HIS A:265 , PO4 A:403 , HOH A:506 , HOH A:561 , ARG B:204BINDING SITE FOR RESIDUE 24G A 402
03AC3SOFTWARELEU A:62 , GLU A:78 , HIS A:79 , THR A:191 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:401 , 24G A:402BINDING SITE FOR RESIDUE PO4 A 403
04AC4SOFTWAREHIS B:79 , HIS B:238 , ASP B:242 , PO4 B:403BINDING SITE FOR RESIDUE ZN B 401
05AC5SOFTWAREARG A:204 , THR B:60 , LEU B:62 , LYS B:143 , ILE B:159 , ASP B:160 , PHE B:161 , PHE B:192 , PHE B:194 , CYS B:207 , SER B:211 , VAL B:217 , LYS B:239 , LYS B:262 , GLY B:264 , HIS B:265 , PO4 B:403 , HOH B:502 , HOH B:512 , HOH B:521 , HOH B:528 , HOH B:534 , HOH B:536BINDING SITE FOR RESIDUE 24G B 402
06AC6SOFTWARELEU B:62 , THR B:76 , GLU B:78 , HIS B:79 , THR B:191 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:401 , 24G B:402BINDING SITE FOR RESIDUE PO4 B 403
07AC7SOFTWAREHIS C:79 , HIS C:238 , ASP C:242 , PO4 C:403BINDING SITE FOR RESIDUE ZN C 401
08AC8SOFTWARETHR C:60 , LEU C:62 , ILE C:159 , PHE C:161 , PHE C:192 , ILE C:198 , CYS C:207 , GLY C:210 , SER C:211 , ALA C:215 , VAL C:217 , LYS C:239 , LYS C:262 , GLY C:264 , HIS C:265 , PO4 C:403 , ARG D:204BINDING SITE FOR RESIDUE 24G C 402
09AC9SOFTWAREGLU C:78 , HIS C:79 , THR C:191 , HIS C:238 , ASP C:242 , HIS C:265 , ZN C:401 , 24G C:402BINDING SITE FOR RESIDUE PO4 C 403
10BC1SOFTWAREHIS D:79 , HIS D:238 , ASP D:242 , PO4 D:403BINDING SITE FOR RESIDUE ZN D 401
11BC2SOFTWAREARG C:204 , LEU D:18 , LEU D:62 , LYS D:143 , ILE D:159 , ASP D:160 , PHE D:161 , THR D:191 , PHE D:192 , PHE D:194 , GLY D:210 , SER D:211 , ALA D:215 , VAL D:217 , LYS D:239 , LYS D:262 , GLY D:264 , HIS D:265 , PO4 D:403 , HOH D:501BINDING SITE FOR RESIDUE 24G D 402
12BC3SOFTWARETHR D:76 , GLU D:78 , HIS D:79 , THR D:191 , HIS D:238 , ASP D:242 , HIS D:265 , ZN D:401 , 24G D:402BINDING SITE FOR RESIDUE PO4 D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MDT)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:45 -Pro A:46
2Asn B:45 -Pro B:46
3Asn C:45 -Pro C:46
4Asn D:45 -Pro D:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MDT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MDT)

(-) Exons   (0, 0)

(no "Exon" information available for 4MDT)

(-) 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:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eee.....eee.hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee....hhhhhhh..eeeee.hhhhhhhhh.....eeehhhhhhhhhh......hhhhheee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mdt A   1 MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKAP 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


Chain B from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eee.....ee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheeeeeee..eeee...eeeee..eeeeee....eeeeee......hhhhh..eeeee.hhhhhhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mdt B   1 MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKAP 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


Chain C from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eee.....eee.hhhhhhhhhhhh...eeeee...........hhhhhhhhhhh.eeeeeee..eeee...eeeee..eeeeee....eeeeee............eeee..hhhhhhhh......eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhh...eeee........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdt C   1 MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKAP 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160      |171       181       191       201       211       221       231       241       251       261       271       281       291         
                                                                                                                                                                                                167|                                                                                                                                   
                                                                                                                                                                                                 169                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeee......eeeeeeee......eeeee......eeee.hhh.eee.....eee.....ee..hhhhhhhhhhh....eeeee...........hhhhhhhhhhhheee......eeee...eeeee..eeeeee....eeeeee......hhhhh...eeee.hhhhhhhhh.....eeehhhhhhhhh............eee..............hhhhhhhhhhhhhhhhhhh.eeeeeeeee..hhhhhhhhhhhhhhhhh.eeee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mdt D   4 QRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPIMDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLA 296
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   Legend:   → Mismatch (orange background)
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  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 4MDT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MDT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MDT)

(-) Gene Ontology  (10, 10)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXC_ECOLI | P0A725: 4is9 4isa 4mqy

(-) Related Entries Specified in the PDB File

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