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(-) Description

Title :  NUCLEOTIDE SUBSTRATE BINDING BY UDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE
 
Authors :  V. Ulaganathan, L. Buetow, W. N. Hunter
Date :  25 Jan 07  (Deposition) - 24 Apr 07  (Release) - 04 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Lipid A Biosynthesis, Transferase, Acyltransferase, Lipid Synthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Ulaganathan, L. Buetow, W. N. Hunter
Nucleotide Substrate Recognition By Udp-N- Acetylglucosamine Acyltransferase (Lpxa) In The First Step Of Lipid A Biosynthesis.
J. Mol. Biol. V. 369 305 2007
PubMed-ID: 17434525  |  Reference-DOI: 10.1016/J.JMB.2007.03.039

(-) Compounds

Molecule 1 - ACYL-[ACYL-CARRIER-PROTEIN]--UDP-N- ACETYLGLUCOSAMINE O-ACYLTRANSFERASE
    ChainsA
    EC Number2.3.1.129
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET15B
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymUDP-N-ACETYLGLUCOSAMINE ACYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:220 , ARG A:224 , HOH A:2106 , HOH A:2193 , HOH A:2392 , HOH A:2393 , HOH A:2394 , HOH A:2395 , HOH A:2398BINDING SITE FOR RESIDUE EDO A1264
2AC2SOFTWAREGLY A:79 , GLY A:196 , VAL A:197 , ILE A:199 , ARG A:216 , HOH A:2278 , HOH A:2391 , HOH A:2392 , HOH A:2397BINDING SITE FOR RESIDUE PEG A1263

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2JF2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:190 -His A:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LPXA_ECOLI_001 *G189SLPXA_ECOLI  ---  ---AG189S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LPXA_ECOLI_001 *G189SLPXA_ECOLI  ---  ---AG189S
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.LPXA_ECOLI20-48
153-181
  2A:20-48
A:153-181
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.LPXA_ECOLI20-48
153-181
  6A:20-48
A:153-181

(-) Exons   (0, 0)

(no "Exon" information available for 2JF2)

(-) 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:264
 aligned with LPXA_ECOLI | P0A722 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:264
                              1                                                                                                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    
           LPXA_ECOLI     - --MIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
               SCOP domains d2jf2a_ A: UDP N-acetylglucosamine acyltransferase                                                                                                                                                                                                                       SCOP domains
               CATH domains 2jf2A01 A:-1-196 Hexapeptide repeat proteins                                                                                                                                                          2jf2A02 A:197-262  [code=1.20.1180.10, no name defined]            CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A02 A:108-143           ------------------------------------Acetyltransf_11-2jf2A01 A:180-262                                                   Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A03 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A04 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A05 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------------------------------------Hexapep-2jf2A06 A:108-143           ----------------------------------------------------------------------------------------------------------------------- Pfam domains (5)
         Sec.struct. author ........ee....ee....ee....ee....ee...eee....ee....ee..eeee....ee....eeee............eeee....ee....eee........eeee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee.......eeee....eeeeehhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2jf2 A  -1 GSMIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVVNGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHRGTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDFAIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIEGLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFTDFFARSTRGLIR 262
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258    

   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, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric Unit

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (LPXA_ECOLI | P0A722)
molecular function
    GO:0008780    acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity    Catalysis of the reaction: (R)-3-hydroxytetradecanoyl-[acyl-carrier protein] + UDP-N-acetylglucosamine = [acyl-carrier protein] + UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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:0008610    lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LPXA_ECOLI | P0A7221lxa 2aq9 2jf3 2qia 2qiv 4j09

(-) Related Entries Specified in the PDB File

1lxa UDP N-ACETYLGLUCOSAMINE ACYLTRANSFERASE
2aq9 STRUCTURE OF E. COLI LPXA WITH A BOUND PEPTIDE THAT ISCOMPETITIVE WITH ACYL-ACP
2jf3 NUCLEOTIDE SUBSTRATE BINDING BY UDP-N- ACETYLGLUCOSAMINE ACYLTRANSFERASE