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

(-) Description

Title :  CRYSTAL STRUCTURE OF E.COLI ARNA TRANSFORMYLASE DOMAIN
 
Authors :  P. Z. Gatzeva-Topalova, A. P. May, M. C. Sousa
Date :  04 Feb 05  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Rossmann Fold; Ob-Like Fold, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Z. Gatzeva-Topalova, A. P. May, M. C. Sousa
Crystal Structure And Mechanism Of The Escherichia Coli Arna (Pmri) Transformylase Domain. An Enzyme For Lipid A Modification With 4-Amino-4-Deoxy-L-Arabinose And Polymyxin Resistance.
Biochemistry V. 44 5328 2005
PubMed-ID: 15807526  |  Reference-DOI: 10.1021/BI047384G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN ARNA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMS195
    Expression System StrainROSETTA (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePTYB2
    FragmentTRANSFORMYLASE DOMAIN
    GeneYFBG
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymHYPOTHETICAL PROTEIN YFBG

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YRW)

(-) Sites  (0, 0)

(no "Site" information available for 1YRW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Leu A:108 -Pro A:109
2Asp A:226 -Pro A:227
3Ala A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YRW)

(-) 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:291
 aligned with ARNA_ECOLI | P77398 from UniProtKB/Swiss-Prot  Length:660

    Alignment length: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
           ARNA_ECOLI     1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTDNPGEKAFYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHPHASKAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQ 300
               SCOP domains d1yrwa2 A:1-203 Polymyxin resistan      ce protein ArnA, N-terminal domain                                                                                                                                 d1yrwa1 A:204-300 Polymyxin resistance protein    ArnA, domain 2                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------Formyl_trans_N-1yr      wA02 A:17-177                                                                                                                            ----------------------Formyl_trans_C-1yrwA01 A:200-297                                                                  --- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhh..eeeeee....------...hhhhhhhhhh..ee......hhhhhhhhhhhh..eeeee......hhhhhh.....eeeee.......ee.hhhhhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhh.ee...hhhhhh.....hhhhhhhhhhhh......eeeee..eeeeeeeeeee.---......eee...eeee....eeeeeeeee.....eehhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yrw A   1 MKTVVFAYHDMGCLGIEALLAAGYEISAIFTHTD------FYGSVARLAAERGIPVYAPDNVNHPLWVERIAQLSPDVIFSFYYRHLIYDEILQLAPAGAFNLHGSLLPKYRGRAPLNWVLVNGETETGVTLHRMVKRADAGAIVAQLRIAIAPDDIAITLHHKLCHAARQLLEQTLPAIKHGNILEIAQRENEATCFGRRTPDDSFLEWHKPASVLHNMVRAVADPWPGAFSYVGNQKFTVWSSRVHP---KAQPGSVISVAPLLIACGDGALEIVTGQAGDGITMQGSQLAQTLGLVQ 300
                                    10        20        30   |     -|       50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        |-  |    260       270       280       290       300
                                                            34     41                                                                                                                                                                                                             249 253                                               

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YRW)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ARNA_ECOLI | P77398)
molecular function
    GO:0070403    NAD+ binding    Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0099619    UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity    Catalysis of the reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-beta-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-beta-L-arabinopyranose
    GO:0048040    UDP-glucuronate decarboxylase activity    Catalysis of the reaction: H(+) + UDP-alpha-D-glucuronate = CO(2) + UDP-alpha-D-xylose.
    GO:0099618    UDP-glucuronic acid dehydrogenase activity    Catalytis of the reaction: UDP-glucuronate + NAD+ = UDP-beta-L-threo-pentapyranos-4-ulose + CO2 + NADH + H+
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0016742    hydroxymethyl-, formyl- and related transferase activity    Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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.
biological process
    GO:0033320    UDP-D-xylose biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-D-xylose, uridinediphosphoxylose, a substance composed of xylose in glycosidic linkage with uridine diphosphate.
    GO:0009058    biosynthetic process    The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
    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:0046493    lipid A metabolic process    The chemical reactions and pathways involving 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:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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.

 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 1yrw)
 
  Sites
(no "Sites" information available for 1yrw)
 
  Cis Peptide Bonds
    Ala A:263 - Pro A:264   [ RasMol ]  
    Asp A:226 - Pro A:227   [ RasMol ]  
    Leu A:108 - Pro A:109   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1yrw
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  ARNA_ECOLI | P77398
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  ARNA_ECOLI | P77398
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARNA_ECOLI | P773981u9j 1z73 1z74 1z75 1z7b 1z7e 2bll 2bln 4wkg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1YRW)