Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF LPXD FROM ESCHERICHIA COLI
 
Authors :  C. M. Bartling, C. R. H. Raetz
Date :  11 Sep 08  (Deposition) - 18 Aug 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lpxd, Acyltransferase, Left-Handed Parallel Beta Helix, Acyl Carrier Protein, Antibiotic Resistance, Lipid A Biosynthesis, Lipid Synthesis, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Bartling, C. R. Raetz
Crystal Structure And Acyl Chain Selectivity Of Escherichia Coli Lpxd, The N-Acyltransferase Of Lipid A Biosynthesis
Biochemistry V. 48 8672 2009
PubMed-ID: 19655786  |  Reference-DOI: 10.1021/BI901025V
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N- ACYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11D
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LPXD, FIRA, OMSA, B0179, JW0174
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: W3110
    Synonym: PROTEIN FIRA, RIFAMPICIN RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3EH0)

(-) Sites  (0, 0)

(no "Site" information available for 3EH0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EH0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EH0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EH0)

(-) PROSITE Motifs  (1, 12)

Asymmetric/Biological Unit (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.LPXD_ECOLI100-128
 
 
106-134
 
 
130-158
 
 
225-253
 
 		  12A:100-128
B:100-128
C:100-128
A:106-134
B:106-134
C:106-134
A:130-158
B:130-158
C:130-158
A:225-253
B:225-253
C:225-253

(-) Exons   (0, 0)

(no "Exon" information available for 3EH0)

(-) 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:341
 aligned with LPXD_ECOLI | P21645 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    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       310       320       330       340 
           LPXD_ECOLI     1 MPSIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhh..eee.....ee.ee.........eeee....hhhhhhhhh...eeee...hhhhh...eee..hhhhhhhhhhhhhh.............ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....eeee....eeee..eeee......eee....ee....eee......eee....ee....ee....ee....ee....ee...eee....ee....ee...eee...eee....ee.......eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         -HEXAPEP_TRANSFERASES         ------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh0 A   1 MASIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
                                    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       310       320       330       340 


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with LPXD_ECOLI | P21645 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    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       310       320       330       340 
           LPXD_ECOLI     1 MPSIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhh.ee......ee.ee.........eeee....hhhhhh......eeeee.hhhhhh..eeeee.hhhhhhhhhhhhh..............ee....ee....ee....ee....ee....ee....ee....ee....ee....ee...eee....ee....eeee....eee....eee......eee....ee....eee......eee....ee....ee....ee....ee....ee...eee....ee....ee...eee...eee....ee.......eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         -HEXAPEP_TRANSFERASES         ------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh0 B   1 MASIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
                                    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       310       320       330       340 


Chain C from PDB  Type:PROTEIN  Length:341
 aligned with LPXD_ECOLI | P21645 from UniProtKB/Swiss-Prot  Length:341

    Alignment length:341
                                    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       310       320       330       340 
           LPXD_ECOLI     1 MPSIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhh..eee.....ee.ee.........eeee..hhhhhhhhhhh...eeee...hhhhh..eeee..hhhhhhhhhhhhh..............ee....ee....ee....ee....ee....ee....ee....ee....ee....ee...eee....ee....eeee....eeee..eeee......eee....ee....eee......eee....ee....ee....ee....ee....ee...eee....ee....ee...eee...eee....ee.......eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         -HEXAPEP_TRANSFERASES         ------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eh0 C   1 MASIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLGLCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAPSAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGSRLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVIIGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGGVIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYSSGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKVNQQD 341
                                    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       310       320       330       340
   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 3EH0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EH0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EH0)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (LPXD_ECOLI | P21645)
molecular function
    GO:0016410    N-acyltransferase activity    Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule.
    GO:0103118    UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity    Catalysis of the reaction: UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine(1-) + an (3R)-3-hydroxymyristoyl-[acp] <=> UDP-2,3-bis[O-(3R)-3-hydroxymyristoyl]-alpha-D-glucosamine + H+ + a holo-[acyl-carrier protein]
    GO:0043764    UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase activity    Catalysis of the reaction: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl-[acyl-carrier protein] = UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl-carrier protein].
    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).
    GO:0016747    transferase activity, transferring acyl groups other than amino-acyl groups    Catalysis of the transfer of an acyl group, other than amino-acyl, 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: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.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3eh0)
 
  Sites
(no "Sites" information available for 3eh0)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3eh0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3eh0
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LPXD_ECOLI | P21645
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LPXD_ECOLI | P21645
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LPXD_ECOLI | P21645: 4ihf 4ihg 4ihh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3EH0)