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(-) Description

Title :  4FE-4S-PYRUVATE FORMATE-LYASE ACTIVATING ENZYME IN COMPLEX WITH ADOMET AND A PEPTIDE SUBSTRATE
 
Authors :  J. L. Vey, C. L. Drennan
Date :  21 Feb 08  (Deposition) - 28 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.77
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Adomet Radical, Sam Radical, Activase, Glycyl Radical, Partial Tim Barrel, 4Fe-4S, Carbohydrate Metabolism, Cytoplasm, Glucose Metabolism, Iron, Iron-Sulfur, Metal- Binding, Oxidoreductase, S-Adenosyl-L-Methionine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Vey, J. Yang, M. Li, W. E. Broderick, J. B. Broderick, C. L. Drennan
Structural Basis For Glycyl Radical Formation By Pyruvate Formate-Lyase Activating Enzyme.
Proc. Natl. Acad. Sci. Usa V. 105 16137 2008
PubMed-ID: 18852451  |  Reference-DOI: 10.1073/PNAS.0806640105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRUVATE FORMATE-LYASE 1-ACTIVATING ENZYME
    ChainsA
    EC Number1.97.1.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCAL-N-AE
    Expression System StrainBL21(DE3)PLYSS
    Expression System Vector TypePLASMID
    GenePFLA
    Organism ScientificESCHERICHIA COLI
    SynonymPFL-ACTIVATING ENZYME, FORMATE-C- ACETYLTRANSFERASE-ACTIVATING ENZYME 1
 
Molecule 2 - PEPTIDE SUBSTRATE VSGYAV
    ChainsB
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS SYNTHESIZED BY CELTEK PEPTIDES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2NA1Ligand/IonSODIUM ION
3SAM1Ligand/IonS-ADENOSYLMETHIONINE
4SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:104 , THR A:105 , MET A:127 , ASP A:129BINDING SITE FOR RESIDUE NA A 820
2AC2SOFTWARETYR A:35 , CYS A:36 , HIS A:37 , ASN A:38 , SER A:76 , GLY A:77 , GLY A:78 , GLU A:79 , ASP A:104 , THR A:105 , ASP A:129 , LYS A:131 , LEU A:199 , PRO A:200 , TYR A:201 , HIS A:202 , SER B:733BINDING SITE FOR RESIDUE SAM A 501
3AC3SOFTWARECYS A:29 , MET A:31 , CYS A:33 , CYS A:36 , TRP A:42 , GLY A:78 , ASN A:106BINDING SITE FOR RESIDUE SF4 A 500
4AC4SOFTWAREGLY A:17 , TRP A:164 , ARG A:166 , GLU A:197BINDING SITE FOR RESIDUE FMT A 502
5AC5SOFTWAREASP A:113 , GLU A:214BINDING SITE FOR RESIDUE FMT A 503
6AC6SOFTWAREPHE A:108 , ARG A:110 , ARG A:111BINDING SITE FOR RESIDUE FMT A 504
7AC7SOFTWAREARG A:32 , ARG A:110BINDING SITE FOR RESIDUE FMT A 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CB8)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RADICAL_ACTIVATINGPS01087 Radical activating enzymes signature.PFLA_ECOLI18-39  1A:17-38

(-) Exons   (0, 0)

(no "Exon" information available for 3CB8)

(-) 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:244
 aligned with PFLA_ECOLI | P0A9N4 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
           PFLA_ECOLI     3 VIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYGHKVMF 246
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.......eeeeee...........hhhhh.....eeehhhhhhhhhh.hhhhhhhhh.eeeeee.hhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhh..eeeee....hhhhhhhhh...hhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhhhhhh..eeeeeeee.....hhhhhh.............hhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------RADICAL_ACTIVATING    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cb8 A   2 VIGRIHSFESCGTVDGPGIRFITFFQGCLMRCLYCHNRDTWDTHGGKEVTVEDLMKEVVTYRHFMNASGGGVTASGGEAILQAEFVRDWFRACKKEGIHTCLDTNGFVRRYDPVIDELLEVTDLVMLDLKQMNDEIHQNLVGVSNHRTLEFAKYLANKNVKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVEKIELLPYHELGKHKWVAMGEEYKLDGVKPPKKETMERVKGILEQYGHKVMF 245
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    

Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3cb8 B 732 VSGYAV 737

   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 3CB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CB8)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PFLA_ECOLI | P0A9N4)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0043365    [formate-C-acetyltransferase]-activating enzyme activity    Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical.
    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:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0018307    enzyme active site formation    The modification of part of an enzyme to form the active site.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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.
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 Specified in the PDB File

3c8f 4FE-4S-PYRUVATE FORMATE-LYASE ACTIVATING ENZYME WITH PARTIALLY DISORDERED ADOMET