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The Open Protein Structure Annotation Network
PDB Keyword
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3n0v

    Title Crystal structure of a formyltetrahydrofolate deformylase (PP_0327) from PSEUDOMONAS PUTIDA KT2440 at 2.25 A resolution. To be published
    Site JCSG
    PDB Id 3n0v Target Id 398629
    Molecular Characteristics
    Source Pseudomonas putida kt2440
    Alias Ids TPS29656,NP_742494.1, _0004.004077_, 323476 Molecular Weight 32440.40 Da.
    Residues 285 Isoelectric Point 6.19
    Sequence msrapdtwiltadcpsmlgtvdvvtrylfeqrcyvtehhsfddrqsgrffirvefrqpddfdeagfrag laerseafgmafeltapnhrpkvvimvskadhclndllyrqrigqlgmdvvavvsnhpdleplahwhki pyyhfaldpkdkpgqerkvlqvieetgaelvilarymqvlspelcrrldgwainihhsllpgfkgakpy hqaynkgvkmvgatahyinndldegpiiaqgvevvdhshypedliakgrdiecltlaravgyhierrvf lnanrtvvl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.25 Rfree 0.274
    Matthews' coefficent 2.76 Rfactor 0.222
    Waters 424 Solvent Content 55.48

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3n0v
    1. Distributed structure determination at the JCSG
    H van den Bedem, G Wolf, Q Xu - Section D: Biological , 2011 - scripts.iucr.org
     
    2. Crystal structure of tandem ACT domain_containing protein ACTP from Galdieria sulphuraria
    E Bitto, DJ Kim, CA Bingman, HJ Kim - Proteins: Structure, , 2012 - Wiley Online Library
     

    Protein Summary

     The protein NP_742494.1 is annotated as formyltetrahydrofolate deformylase. NP_742494.1 belongs to PFAM PF00551 Formyl_trans_N which is a family of Formyl transferase.

    The monomer structure consists of two domains: an N-terminal domain and a C-terminal domain that is very similar to Phosphoribosylglycinamide Formyltransferase and Glycinamide Ribonucleotide Transformylase (see the DALI table below).

    MI15949E_monomer.png 

    The protein assebles as a tetramer in which each monomer make a contact with the other three members of the tetramer.

     MI15949E_tetramer.png

    A DALI search for similar structures returns many hits that all superimpose on the C-terminal domain of the protein. This is shown below in this table.

    DALI Structural Homologs with full length protein
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1men 23.5 2.1 195 201 25 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    2 1rc1 23.3 2.1 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    3 1rbq 23.3 2.1 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    4 1zly 23.2 2.2 194 200 25 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    5 1rby 23.2 2.1 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    6 1rbm 23.2 2.1 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    7 1njs 23.2 2.1 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    8 1zlx 23.1 2.2 194 200 25 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    9 1rc0 23.0 2.2 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    10 1rbz 22.9 2.2 193 200 23 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    11 1c3e 22.5 1.9 194 209 22 GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
    12 1mej 22.4 2.1 195 201 25 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    13 1jkx 22.4 2.0 194 209 22 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    14 1c2t 22.4 1.9 194 209 22 GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
    15 1cde 22.3 2.0 194 210 22 PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE
    16 1gar 22.2 1.8 187 204 23 GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
    17 2ywr 22.1 2.0 195 216 24 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    18 3kcq 21.9 2.0 191 207 26 PHOSPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE
    19 3gar 21.9 2.2 194 209 22 GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE
    20 1meo 21.8 2.1 191 202 23 PHOSOPHORIBOSYLGLYCINAMIDE FORMYLTRANSFERASE

    MI15949E_all.png

    Color scheme: NP_742494.1 (green), 1c2t (cyan), 1c3e (lightmagenta), 1cde (yellow), 1gar (salmon), 1jkx (lightgrey), 1mej (slate), 1men (orange), 1meo (lime), 1njs (deepteal), 1rbm (hotpink), 1rbq (yelloworange), 1rby (violetpurple), 1rbz (grey70), 1rc0 (marine), 1rc1 (olive), 1zlx (smudge), 1zly (teal), 2ywr (dirtyviolet), 3gar (wheat), 3kcq (deepsalmon)

    Only this protein has the extra N-terminal domain shown in green.
     

     

    A narrower search with just the N-terminal domain returns the following hits.

    DALI Structural Homologs for N-terminal domain
    N PDB Z-score RMSD LALI NRES %ID TITLE
    1 1zpv 12.6 1.7 79 85 11 ACT DOMAIN PROTEIN
    2 1u8s 11.5 1.9 78 171 10 GLYCINE CLEAVAGE SYSTEM TRANSCRIPTIONAL
    3 3dc2 10.7 1.9 74 524 11 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    4 3ddn 10.6 2.0 74 525 11 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    5 1ygy 10.6 1.9 74 527 11 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    6 2pa3 9.6 1.8 74 406 7 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    7 1yba 9.5 1.9 74 406 7 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    8 2p9e 9.4 1.9 74 403 7 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    9 2p9c 9.4 1.9 74 405 7 D-3-PHOSPHOGLYCERATE DEHYDROGENASE
    10 2f1f 9.4 2.7 78 158 6 ACETOLACTATE SYNTHASE ISOZYME III SMALL SUBUNIT

    The N-terminal matches well with 1zpv which is an ACT domain protein.

    N-term_1zpv.png N-terminal domain (green), 1zpv (magenta)

     "‘ACT domain’, a novel ligand-binding domain, was recently identified by a PSI-BLAST search. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like βαββαβ topology.  The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory ligand binding fold."

    -- Chipman DM, Shaanan B., The ACT domain family., Curr Opin Struct Biol. 2001 Dec;11(6):694-700.

     

    Ligand Summary

    Reviews

    References

     

    No references found.

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