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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ARNA (PMRI) DECARBOXYLASE DOMAIN
 
Authors :  P. Z. Gatzeva-Topalova, A. P. May, M. C. Sousa
Date :  09 Aug 04  (Deposition) - 26 Oct 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (6x)
Keywords :  Decarboxylase; X-Ray Structure; E. Coli Proteome, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Z. Gatzeva-Topalova, A. P. May, M. C. Sousa
Crystal Structure Of Escherichia Coli Arna (Pmri) Decarboxylase Domain. A Key Enzyme For Lipid A Modification With 4-Amino-4-Deoxy-L-Arabinose And Polymyxin Resistance
Biochemistry V. 43 13370 2004
PubMed-ID: 15491143

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YFBG
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMS122 (AN ENGINEERED VARIANT OF THE PET28)
    Expression System StrainROSETTA (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePMRI, YFBG
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymARNA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A
Biological Unit 3 (6x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:448 , PRO A:595 , ARG A:624BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U9J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U9J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U9J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U9J)

(-) Exons   (0, 0)

(no "Exon" information available for 1U9J)

(-) 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:332
 aligned with ARNA_ECOLI | P77398 from UniProtKB/Swiss-Prot  Length:660

    Alignment length:342
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654  
           ARNA_ECOLI   315 RTRVLILGVNGFIGNHLTERLLREDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLRIIRYCVKYRKRIIFPSTSEVYGMCSDKYFDEDHSNLIVGPVNKPRWIYSVSKQLLDRVIWAYGEKEGLQFTLFRPFNWMGPRLDNLNAARIGSSRAITQLILNLVEGSPIKLIDGGKQKRCFTDIRDGIEALYRIIENAGNRCDGEIINIGNPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVESSSYYGKGYQDVEHRKPSIRNAHRCLDWEPKIDMQETIDETLDFFLRTVDLT 656
               SCOP domains d1u9ja_ A: Polymyxin resistance protein ArnA (PrmI)                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1u9jA01 A:315-508,A:538-568,A:616-634 NAD(P)-binding Rossmann-like Domain                                                                                                                         1u9jA02                      1u9jA01                        1u9jA02 A:509-537,A:569-605,A:635-656----------1u9jA01            1u9jA02                CATH domains
               Pfam domains ---Epimerase-1u9jA01 A:318-566                                                                                                                                                                                                                              ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhh..eeeeeee.....hhhhh....eeeee......hhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..ee..............hhhhhhhhhhhhhh..eeee.....eee.eehhhhhhhhhhhhhhhhhh...eeeee.....eeehhhhhhhhhhhhhh..hhhhh.....eeee..----------.......hhhhhhhhh.....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u9j A 315 RTRVLILGVNGFIGNHLTERLLREDHYEVYGLDIGSDAISRFLNHPHFHFVEGDISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLRIIRYCVKYRKRIIFPSTSEVYGMCSDKYFDEDHSNLIVGPVNKPRWIYSVSKQLLDRVIWAYGEKEGLQFTLFRPFNWMGPRLDNLNAARIGSSRAITQLILNLVEGSPIKLIDGGKQKRCFTDIRDGIEALYRIIENAGNRCDGEIINIGNPENEASIEELGEMLLASFEKHPLRHHFPPFAGFRVVES----------VEHRKPSIRNAHRCLDWEPKIDMQETIDETLDFFLRTVDLT 656
                                   324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604|        - |     624       634       644       654  
                                                                                                                                                                                                                                                                                                                            605        616                                        

   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: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (19, 19)

Asymmetric 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARNA_ECOLI | P773981yrw 1z73 1z74 1z75 1z7b 1z7e 2bll 2bln 4wkg

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