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The Open Protein Structure Annotation Network
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4dqa

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of a hypothetical protein (BACOVA_03559) from Bacteroides ovatus ATCC 8483 at 1.50 A resolution. To be published
    Site JCSG
    PDB Id 4dqa Target Id 416724
    Molecular Characteristics
    Source Bacteroides ovatus atcc 8483
    Alias Ids TPS66813,ZP_02066560.1, 333112 Molecular Weight 39016.67 Da.
    Residues 354 Isoelectric Point 4.89
    Sequence ndllepkvyfeskeynfsvedemdvmtfdlvsrlssatssqvdvsysvaepsvvdeynakygtnyemld vsqvklssttssissgklyadnievelsglealkagnsyvlpmrvhsssvstlsgtniayfffskplki tkagnfsnhyisvkfpvgtffssftyealinvdyfldnntimgtegvmilrigdagggitpkdylevag gqnyrvtkplltnrwyhvaltydqptgktgiyvngekwagsdwgidgfdpnsdmgfyigriygfkwger pfhgkmsevrvwsvartenqlkqnmlgvdpaseglalyykldgsetqeggvikdatgringttngitik tldapiain
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.50 Rfree 0.1764
    Matthews' coefficent 2.53 Rfactor 0.1558
    Waters 438 Solvent Content 51.34

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Hypothetical protein BACOVA_03559 ( TargetDB ID 416724, acession number ZP_02066560.1) is a two domain protein, with a DUF1735 (PF08522) domain (e-value=9.3e-16) at the concanavalin-like lectin/glucanase PFAM clan (CL0004). The best PFAM match is to the Laminin_G_3 Concanavalin A-like lectin/glucanases superfamily Domain (PF13385) (e-value=7.7e-23) at the C-terminal, but more detailed analysis suggests that it may be closer related to another family in this clan, the pentraxin protein domain (PF00354). Proteins of the pentraxin family are involved in acute immunological responses as a pattern recognition receptor (PRRs), which opens interesting possibilitied for function prediction of our BACOVA_03559.

     

    This is one of the several proteins with DUF1735 domain solved by JCSG (3p0z, 3nqk,3n91, 3poh), although BACOVA_03559 seems to be a first protein with this domain combination. We have speculated previously that DUF1735 is a novel carbohydrate binding domain.

     

    monomer.png

     

     


    Shown above is a ribbon representation of the structure of BACOVA_03559 protein, confirming the PFAM analysis.   SCOP,which uses different domain nomenclature, classifies the DUF1735 domain as belonging to the PapD-like Superfamily, which is an example of the  immunoglobilin-like beta sandwich fold. The PapD-like Superfamily includes also proteins belonging to the pilus chaperone family, and the motile major sperm protein-like (MSP-like) family (PF00635).

    A FATCAT search of the PDB_90 database confirms that the BACOVA_03559 structure represents that first example for the structure of a two-domain protein in which a Laminin G_3 Pfam domain is combined with a DUF1735 Pfam domain in a single polypeptide chain. 

     A DALI search using the structure of the N-terminal domain alone, shows similairity to the following targets, including those of some sodium/calcium exchange proteins and periplsamic chaperone-like proteins.

    PDB ID DALI Z-Score rmsd of alignment length of residue alignment total residues in structure match % sequence id Description
    3poh 14.9 2.1 125 435 12 Crystal structure of an endo-beta-N-acetylglucosaminidase (BT_3987) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.55 A resolution
    3po2 12.6 2.5 120 308 18 Crystal structure of a protein of unknown function (BACOVA_00267) from Bacteroides ovatus at 1.55 A resolution
    3nqk 11.6 2.6 118 305 17 Crystal structure of a STRUCTURAL GENOMICS, UNKNOWN FUNCTION (BACOVA_03322) from Bacteroides ovatus at 2.61 A resolution
    3n91 11.5 2.9 121 315 20 Crystal structure of a STRUCTURAL GENOMICS, UNKNOWN FUNCTION (BACOVA_03430) from Bacteroides ovatus at 2.40 A resolution
    3rb7 10.6 2.3 103 242 17

    Crystal structure of CBD12 from CALX1.2 [Ref]

    3gin 10.4 2.2 102 116 14 Crystal structure of E454K-CBD1[Ref]
    3e9u 10.2 2.5 102 162 13 Crystal structure of Calx CBD2 domain[Ref]
    2qvm 10.2 2.4 102 116 9 The second Ca2+-binding domain of the Na+-Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis[Ref]
    3fso 9.7 2.3 98 109 13 Crystal structure of the Calx-beta domain of integrin beta4, calcium soak[Ref]
    2dpk 9.9 2.3 102 124 14 The Crystal Structure of the Primary Ca2+ Sensor of the Na+/Ca2+ Exchanger[Ref]
    2fwu 8.8 2.6 102 157 9 Second Ca2+ binding domain of the Na,Ca-exchanger (NCX1) [Ref]
    1l4i 8.7 2.8 103 189 6 Crystal Structure of the Periplasmic Chaperone SfaE [Ref]
    1qpx 8.6 2.8 103 206 6 CRYSTAL STRUCTURES OF SELF-CAPPING PAPD CHAPERONE HOMODIMERS [Ref]
    3jwn 8.4 2.7 102 199 8 Complex of FimC, FimF, FimG and FimH[Ref]

     

    The C-terminal domain Laminin-like protein shows structural similarity to the following in a DALI search. These structures include some members frim the pentaraxins. Pentraxins are characterized by calcium dependent ligand binding. However, examination of the structure of target ID 416724 in region corresponding to the Ca2+ binding site on related structures, shows that several Glu and Asp residues in the Ca2+-bound pentraxin structures are missing on the 416724 structure.

    PDB ID DALI Z-score rmsd alignment (Ang) length of residues alignment total residues in structure sequence id (%) Description
    2a3w 18.5 2.7 181 204 11 Decameric structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2-carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane[Ref]
    3kqr 18.4 2.8 182 204 12 The structure of serum amyloid p component bound to phosphoethanolamine[Ref]
    2w08 18.4 2.8 182 205 12 THE STRUCTURE OF SERUM AMYLOID P COMPONENT BOUND TO 0-PHOSPHO-THREONINE[Ref]
    2a3y 18.4 2.8 182 204 12 Pentameric crystal structure of human serum amyloid P-component bound to Bis-1,2-{[(Z)-2carboxy-2-methyl-1,3-dioxane]-5-yloxycarbamoyl}-ethane.[Ref]
    1sac 18.2 2.8 182 204 12 THE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT[Ref]
    3d5o 17.9 2.9 182 204 12 Structural recognition and functional activation of FcrR by innate pentraxins[Ref]
    1gyk 17.9 2.8 182 204 12 SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH [Ref]
    1qtj 17.5 2.9 178 217 2 CRYSTAL STRUCTURE OF LIMULUS POLYPHEMUS SAP [Ref]
    3flp 17.5 2.9 177 217 15 Crystal structure of native heptameric SAP-like pentraxin from Limulus polyphemus[Ref]
    1gnh 17.5 2.9 183 206 13 HUMAN C-REACTIVE PROTEIN[Ref]
    1lj7 17.4 2.9 181 206 14 Crystal structure of calcium-depleted human C-reactive protein from perfectly twinned data[Ref]
    1b09 16.8 2.9 182 206 13 HUMAN C-REACTIVE PROTEIN COMPLEXED WITH PHOSPHOCHOLINE[Ref]
    2r16 15.9 2.6 158 175 9 Crystal Structure of bovine neurexin 1 alpha LNS/LG domain 4 (with no splice insert)[Ref]
    3qcw 15.7 2.6 158 1003 9 Structure of neurexin 1 alpha (domains LNS1-LNS6), no splice inserts [Ref]
    3poy 15.4 2.6 158 1005 9 Crystal Structure of the alpha-Neurexin-1 ectodomain, LNS 2-6[Ref]
    2vw1 15.2 2.6 154 658 11 CRYSTAL STRUCTURE OF THE NANB SIALIDASE FROM STREPTOCOCCUS PNEUMONIAE[Ref]
    1dyk 15.1 2.1 150 374 9 LAMININ ALPHA 2 CHAIN LG4-5 DOMAIN PAIR[Ref]
    2h0b 15.0 2.5 155 181 15 Crystal Structure of the second LNS/LG domain from Neurexin 1 alpha [Ref]

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Upon examination of the structure, and comparison with the structures of the top-scoring DALI hits indicates that the putative active site on the C-terminal domain maps to a cluster of conserved residues that include Glu 209, Asp 218, and Arg 215.

    Ligand Summary

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