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The Open Protein Structure Annotation Network
PDB Keyword
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3gz7

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

    Title Crystal structure of Putative antibiotic biosynthesis monooxygenase (NP_888398.1) from BORDETELLA BRONCHISEPTICA at 2.15 A resolution. To be published
    Site JCSG
    PDB Id 3gz7 Target Id 390479
    Molecular Characteristics
    Source Bordetella bronchiseptica rb50
    Alias Ids TPS20148,NP_888398.1, 3.30.70.900, 85589 Molecular Weight 11025.01 Da.
    Residues 96 Isoelectric Point 5.66
    Sequence miqeiasilvqpgreadfeagvaqarplfmrargchgvalhrsieapqrytlvvdwetvdnhmvdfrqs adfqewrklvgecfaeppqvhheqkvl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.15 Rfree 0.236
    Matthews' coefficent 2.15 Rfactor 0.174
    Waters 145 Solvent Content 42.90

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     Pfam update:This protein is now in family PF03992.9 ABM, CL0032, and there are other structures.

    This protein is annotated as a hypothetical protein BB1853 [Bordetella bronchisept
    ica RB50] in PSCA. It belongs Pfam; PF03992; Antibiotic Biosynthesis Monooxygenase (ABM) family.

    It is present as a dimer in the crystal structure and crystal packing analysis suggests that this dimer should be the stable oligomeric  form in solution.

     

    Fig1_MG7794B.png

        Fig 1. Dimer of 390479 in asu.

     

    The 390479 is structurally similar to 1lq9 ( Dali Z=12.2, 2.5A rmsd, 12 %id). The comparison of the active site of 390479 (green) with 1lq9 (light blue) shows a match on Trp 56 (Trp 66) residue. The details are shown below.   

     

    FIg2_MG7794B (1).png

      Fig 2. From left top Leu52 (Asn 62), Leu 40- green (Tyr 51- light blue).

                From left bottom His 62 (Tyr 72 -dual conf.) and Typ 56 (Trp 66) of 390479 - green (1lq9- light blue).

                (Citrate ligand is not shown in this Fig.)

     

     

    FIg2_MG7794B_CIT.png

     

     Fig. 3. The same view as Fig 2 with a citrate molecule in the active site.

               A citrate molecule (CIT- pink, ball-and-stick model) is modeled in the active site of both A and

               B molecules of 390479 (green).

     

     

    FFAS Hits are:

     

    # Score Template Links and tools %id First MIQEIASILVQPGREADFEAGVAQARPLFMRARGCHGVALHRSIEAPQRYTLVVDWETVDNHMVDFRQSADFQEWRKLVGECFAEPPQVHHEQKVL Last
    1 -58.300 3gz7_A mol:protein length:115 Putative antibiotic biosynthesis monooxygenas  ali model follow..  100  14 MIQEIASILVQPGREADFEAGVAQARPLFMRARGCHGVALHRSIEAPQRYTLVVDWETVDNHMVDFRQSADFQEWRKLVGECFAEPPQVHHEQKVL 109
    2 -51.200 2gff_A mol:protein length:106 LsrG Protein  ali model follow..  10  1 MHVTLVEINVKEDKVDQFIEVFRANHLGSIREAGNLRFDVLRDEHIPTRFYIYEAYTDEAA-VAIHKTTPHYLQCVEQLAPLMTGPRKKTVFIGL. 94
    3 -50.200 4dpo_A mol:protein length:119 Conserved protein  ali model follow..  20  19 AIRVVAKNQVKPEKVQEFMNLCKSLIEETLKEEGCIDYGVYQELENPEILTMLEEWKDEGS-LDQHIRSDHFKEIFPLLSECLDKETEINIYRKKL 113
    4 -49.800 2bbe_A mol:protein length:108 hypothetical protein SO0527  ali model follow..  23  13 QIVCVASFLSKEGKTEALIAALASLIPDTRREAGCIRYELNVSRDEPRRVTFVEKFVDIAA-FDEHCAKDAIQHYFHQVMPELVESFHVETYHQV. 106
    5 -49.700 3qmq_A mol:protein length:99 Autoinducer-2 (AI-2) modifying protein LsrG  ali model follow..  10  4 MHVTLVEINVHEDKVDEFIEVFRQNHLGSVQEEGNLRFDVLQDPEVNSRFYIYEAYKDEDA-VAFHKTTPHYKTCVAKLESLMTGPRKKRLFNGLM 98
    6 -49.500 2fb0_A mol:protein length:94 conserved hypothetical protein  ali model follow..  10  4 MIRLNVFVRVNETNREKAIEAAKELTACSLKEEGCIAYDTFESSTRRDVFMICETWQNAEV-LAAHEKTAHFAQYVGIIQELAEMKLEKFEF.... 94
    7 -48.700 4hl9_A mol:protein length:118 Antibiotic biosynthesis monooxygenase  ali model follow..  12  17 MLKVIAQDFIKPEAIDIVLPLYRELVEKTRQEPLCLAYDLFVDQKDPGHFVFIEEWPDRAA-LDIHCATEHFTRLVPLINAHQRQDGTVVLMDAV. 110
    8 -48.700 2omo_A mol:protein length:124 DUF176  ali model follow..  19  17 MYVTIVYASVKTDKTEAFKEATRMNHEQSIREPGNMRFDILQSADDPTRFVLYEAYKTRKD-AAAHKETAHYLTWRDTVADWMAEPRKGVIYGGL. 110
    9 -47.300 3e8o_A mol:protein length:119 uncharacterized protein with ferredoxin-like  ali model follow..  19 MVISHGTLSASAEHAAHLRQLLVHIAQATRQEDGCLLYLVSEDLSQPGHFLITEHWDNLGA-MHTHLALPGVTQAIDALKHLNVTDLKITAYEAG. 112
    10 -47.200 3bm7_A mol:protein length:115 Protein of unknown function with ferredoxin-l  ali model follow..  22  14 MIGVVATLKVQPAKAAEFEKVFLDLAAKVKAEPGCLVYQLTRSKTEEGVYKVLELYASMDA-LKHHGGTDYFKAAGAAMGPTMAGAPVIEYLDAV. 108
    11 -46.300 1x7v_A mol:protein length:99 PA3566 protein  ali model follow..  13  6 PLTLIATITAAPGHAEALERELRALVAPSRAEAGCLQYDLHQDRHDSHLFYMIEQWRDDAA-LERHQNTEHFLRFSRGNEALLQNVKIDQLYR... 97
    12 -46.100 1y0h_A mol:protein length:102 hypothetical protein Rv0793  ali model follow..  18  5 PVAVIARFMPRPDARSALRALLDAMITPTRAEDGCRSYDLYES-ADGGELVLFERYRSRIA-LDEHRGSPHYLNYRAQVGELLTRPVAVTVLAPL. 97
    13 -45.900 1iuj_A mol:protein length:106 hypothetical protein TT1380  ali model follow..  22  1 MFVTMNRIPVRPEYAEQFEEAFRQRARLVDRMPGFIRNLVLRPKNPGDPYVVMTLWESEEA-FRAWTESPAFKEGHARSGTLFLGPNRLEAFEVVL 99
    14 -44.800 4dn9_A mol:protein length:122 Antibiotic biosynthesis monooxygenase  ali model follow..  14  17 MYGLIGKMRATPGQRDALIAIL---VEGASSMPGCLSYVVAQDPKDPDAIWITEVWDSPES-HKASLSLPSVQDAIACGRPLIAALDEHHETVPV. 107
    15 -44.100 2pd1_A mol:protein length:104 Hypothetical protein  ali model follow..  13  5 KLALFVRLEAKPGQEAALADFLASALPLANAESGTTAWFALK--FGPSTFGVFDAFADEAG-RQAHLNGQIAAALMANAATLLSSPPNIEKVELL. 96
    16 -43.100 3hx9_A mol:protein length:124 Protein Rv3592  ali model follow..  18  3 .VVKINAIEVPAGAGPELEKRFAHRAHAVENSPGFLGFQLLRPVKGEERYFVVTHWESDEA-FQAWANGPAIAAHAGHRANPVATGASLLEFEVV. 95
    17 -42.800 3kkf_A mol:protein length:105 Putative antibiotic biosynthesis monooxygenas  ali model follow..  5 NMVRLSRIIIDPERLEEYNAYLKEEIESMRLEPGVLVLYAVAEKERPNHVTILEIYADEAA-YKSHIATPHFKKYKEGTLDMVQMLELIDA..... 95
    18 -42.600 1q8b_A mol:protein length:105 Protein yjcS  ali model follow..  13 MHYITACLKIISDKDNEIMKEFKKLEEETNKEEGCITFHAYPLEPSERKIMLWEIWENEEA-VKIHFTKKHTIDVQKQELTEVEWLMKSNVND... 105
    19 -42.500 3fgv_A mol:protein length:106 uncharacterized protein with ferredoxin-like  ali model follow..  16  15 .EVVIVKSTPQRGKFNAFAELVGKLVSETRDFPGCLGAYLMLA-PERNEQVVMHIWETPDA-LEAYLTWRADRGDFLEINEYLEVEQDFKTYQ... 104

    Ligand Summary

     

    Citrate (CIT) molecules were modeled based on crystallization conditions.

    Reviews

    References

     

    No references found.

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