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The Open Protein Structure Annotation Network
PDB Keyword
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3bfm

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

    Title Crystal structure of biotin protein ligase-like protein of unknown function (YP_612389.1) from Silicibacter sp. TM1040 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 3bfm Target Id
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    Molecular Characteristics
    Source
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Alias Ids
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    TPS1693,YP_612389.1, 104651
    Molecular Weight
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Da.
    Residues
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Isoelectric Point
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Sequence
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
      BLAST   FFAS

    Structure Determination
    Method XRAY
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Chains 1
    Resolution (Å)
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Rfree
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Matthews' coefficent 2.19 Rfactor 0.179
    Waters
    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)
    Solvent Content 43.80

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 3bfm
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    reference to undefined name 'note' Exception of type 'MindTouch.Deki.Script.Runtime.DekiScriptUndefinedNameException' was thrown. (click for details)

    Protein Summary

    The fold of this structure is very similar to biotin-[acetyl-CoA-carboxylase] ligase. However, there is one significant difference between this structure and all other known structural homologs, this structure does not have so called (b2-b3) insertion (between 43-47) loop which is essential for substrate binding. In many structures with no substrate bound, this loop is flexible. As a result of lacking this loop, the binding site is becoming fully exposed to solvent. Additionally, the essential residues near the biotin binding site are not conserved in this protein. This suggests that FM11526A may have some new function despite a well defined known fold.

    Maybe a dimer, but the dimer is not conserved in structural homologs.

    Sequence alignment between YP_612389.1 and its homologs:
    YP_612389      TITFPPLMTGEAAGP-GQDPFDLACQKAELGVDAGLVVYELGTDVLRAALVLAPEVPLAKAMAMLPVCGVGFQNALGALAPPEVAVHLDWNGALRINGAR
    ZP_01058811 -LSFPPLMSGLAVTG-QEDP
    FETACQRAVLGCDAGLLTYNLGADLLRAALVFAPEVSLHKAMAMLPTCGIGLQNALGALAPPEVAVHLEWGGGLRINGGR
    ZP_01904194 -PAFPPLMSGHPVDA-GIDP
    FEKACAMAALGCDAGLIVHNIAANRLAAALVMAPEVPLEQAMAMLPLCGVGFQNALGALGPPEVAVHLEWAGGLRVNGAS
    ZP_01755469 -PAFPPLMSGDAVSG-QADP
    FEVACQRAVLGCDAGLIVYNLAADRLRAALVFAPEVPLERAMAMLPACGIGFQNALGALAPPEVAMHLEWDGKIRVNGAS
    ZP_01743189 TPSFPPLFSGLAVEG-TIDP
    FDKACAEALRGCDAGLVVYNLGAHTLRASVVFAPDVSLQDAMAMLPLCGVGFQNALGALAPPEVAVHLNWNGALMINGAN
    ZP_01035295 TPSFPPLMSGRAVSG-ATHP
    FDMACTLATQGCDAGLIVHNLTANHLMAAIVLAPEVPLGEAMVMLPTCGVGFQNAFGALAPPEVAVHLEWSGAIRLNGAS
    ZP_01442737 -LAFPPLLWGEAVS---TDA
    FDHACQRALLGCDAGLVAYRVNASVAQAALVFAPEVPLAKAMAMLPLCGVGFQNALGVMAPPEVAVHLDWDGGIRVNGAA
    EDG76557 SLVFPPLMHGYELDKPGHDP
    FEVAKSKAIQGVEAGLVVYNLTHEALRATFIFTPEVSLNQAMIMLPICGIGFQNALGALAPPEVAVHLLWSGGILINGAR
    YP_167041 TPTFPPLMQGVAAQG-GDAP
    FERAQAQAALGCDGGTVVHSVQADRLRAALVLAPEVALADAMAMLPLCAVGFQNALGALAPPEVAVHLDWAGDIHVNGGR
    ZP_00948748 SPVFPPLLTGAQA----EDP
    FAQACAEARQGCDAGLVLYNLGPSVLQAAIVFAPEVPLAQAMAMLPLCAVGFQNALGALAPPEVGVHLAWNGDLRLNGAI
    ZP_01549178 -VQFPPLFQGEALTG-QADP
    FERALALAITGTDPGTVVYNLGGERLRAALIFAPEVPLEQAMAVLPVCGLGFQAALGTLAPPEVAVHLEWDGRIRVNGAV
    YP_683117 -LSFPPLFQGQDTRG--EDP
    LRFACARAASGCDAGLVCHDLRADVLRASLVFAPEVPLQKAAIMLPICGIGFQNALGALAPPEIAVHLDWAGGIRINGGT
    EBF52230 -----------------EDP
    FDAAVKRAIMGCDAGLIAYRLASDKIGAALVLTPEVPLAQAISMLPLCAVAFQNALGALAPPEVAVHLEWAGGLRINGAR
    ZP_01735773 SPQFPPLFSGEVVAK-HTDP
    FDKAVSRAIAGVDSGTIFYSEAVDILRAALVLAPETPLEDAIQAVYVAQIGLAKSLGALAPPEVPVHFEWPDRIKVNGAV
    ZP_00959145 -LTLPPLMWGEAVP---GDA
    FGHAVRRAVLGCDAGLVAYHLGAASIEAALVVAPELPLARAMTMLPLCGVGFQNALGALAPPEVAVHLEWPGAIRVNGAR
    ZP_01893656 SPRLPPLFTGEWVPN-QTDP
    FDKAVSRAIAGVDSGTIFYSDAVDVLRAALVLAPETSLEEAVQVVYVAQIGLAESLGALAPPEVPVFFQWPDRIKVNGAV
    ZP_01748741 -LAFPPAMFGEKVDG---DP
    AETAILRAIQGVDAGLITYRVASDQVGAALVFAPEVPLAQAMTMLPLCGVGFQNALGALAPPEVAVHLGWDSGLRVNGAL
    EDA78152 -PSFPPLFRGKALPL-KKST
    FHNAIEEAKKNIDPGLILYNEDIGELNASIILAPDIKLKQALGMILVNQMGVADSLGSLGPPELAIHFNWPNRIKVNGAN
    EDJ18898 -PTFPPLLKGAECPP-GQDV
    LAKAVAEASLGADPGLTVWRCRPEAMEAAIVLAPDRPLGEAISVAFAVALGLGDALGALAPPEVAVHYDWPGGFRVNGAR
    ECN28793 -----------------------------L
    GCDAGLVVHNLSSDMLRAAIVFAPEVTLEEAMVMLPTCGIGFQNALGALAPPEVAVHLTWDGLILINGAR
    ZP_01749978 --------------------
    MAEAARQATLGCDAGLVTYVSRPDMVEAALVFAPEVPLGKAMAMLPLCGVGFQNALGALGPPEVAAHLEWHGGIRVNAAS
    ECZ46228 -PNFPPLFRGKSLPL-KTTT
    FSKAIEEAKKNIDPGLIIYNEDFGELNASLILAPDIKLKEALGMVLVNQMGLADSLGSLGPPELAIHFNWPNRIKVNGAN
    ECW00844 -PTFPPLLRGEKVGA-TINP
    FQKAVAASVMGTEPGVIYFAEREDMLHLALVLAPETPLSECVGVCHAAMLALADSLGALGPPELAIHFSWPFGLKVNGAH
    EBF28169 -PSFPPLMQGLHAA--GADP
    FDAACKEAEKGCDAGTIVYDITPERLRAAIVFAPEVPLAQAAAMLPLTAVAFQNALGALGPSELPVHLQWDGVVRVNGAQ
    ECZ95388 -PQLPPMFSSQEVLN-GQSV
    FNKAVTAANSG-DVGTVFYSCDEGILNVAITLNPEVIKSKAIQVHYLMTLGLSDTLAALVPPEIEISHIWPNLMFMNRGV
    Consensus/95% ....................h..A...t..sh-sGhlha......h.stllbsP-h.L.pAh.hh.hs.htb.ptLGsLtPPElshab.Wss.bblNtt.


    YP_612389 CGRLRIAASTDDPDTQPDWLVVGLDLPL-WPEG-DGGETPDETALYAEGCADVAAPRLLESWARHCLHWINRWDEGELETIHGEWRGL-AHGMGEART-E
    ZP_01058811
    CGRLRVAASTSDPEAMPDWLVVGLELPL-WPASEDTGETPDQTALYAEGCADVKAPALLESWARHALHWIARWEEDGVEPLHAEWRGL-AHGLGEAGQ-W
    ZP_01904194
    CGRMRAMASTSDATALPDWLVVGLEVPL-LSVGHAPGERPDETALYDEGCADVDATELLEAWARHTLAWITRWEEDGPRALHTDWRGL-AHGIGEDIT-C
    ZP_01755469
    CGLLRAAASSEDPTAAPDWLVIGFDLPL-WPEQEDGGQNPGETALYAEGCAGVSAPDLLESWARHTLHWIARWEEAGNAPLHREWRGL-MHGVGEPVT-R
    ZP_01743189
    CGKLRAAASGNDPLVEPDWIVIGLELPL-WPDSDDTGDQPDQTALYAEGCADVNAVDLLESWIKHSLVGINTWTDGGVTSLHRDWRGL-AHGVGENVA-M
    ZP_01035295
    CGRLRVAAGGTDPEEEPDWLVIGLDLPL-MQIAEHPGDQPDQTSLYDEGCAEIDPVELLEAWARHSLVWINTWEDAGPRALHAEWRGL-AWRMGEEVT-Q
    ZP_01442737
    CGRFRAMASTADPAAVPDWLVIGFTLPL-IPASDRPGDTPDQTSLYAEGCAEVSPHALIEAWARHSLNWINRWDEEGSRALHSEWRGL-AQDMGEEIT-R
    EDG76557
    CGKLRVSANDQDPTKVPDWLCVGLELDL-WPASENMGETPNETALYAEGCSEVDASTLLEAWARHTLNWLTRWEADGVRTVHNEWRGL-AHGIGEKQTYM
    YP_167041
    CGRLCVAASTRDPQVQPDWLVIGLDLAL-LPTSDMPGAHPDETALYEEGCADVTAVTLLESWTRHVMTWINRWEDEGNAPLHAEWMGL-ARGVGEEVT-R
    ZP_00948748
    CGQMRAASSDTDPHHVPDWLVVSFHVKL-LPQSDTPGETPDVTTLYGEGCAEVSPVELLEAWARHMLVALNRWDDEGAGPLHKEWTGL-AWAMGDQIT-Y
    ZP_01549178
    CGRMRVKTSSKDPGGTPDWLILGLELNM-TSRKSSPGKDPERTWLSEEGCGEITAAQLLECWVRHSLYWLNRWLDDGPRPVHAEWRGL-VWAMGETVE-V
    YP_683117
    AGGLKMVASPPSPDQIPDWMVVGLELAL-WPASAETGNTPDVTALISEGCGDVEAPALLEAWVRHTLVWISRWSEDGPRPVHTEWSGL-VHGLGEATQ-M
    EBF52230
    CGGFRAAAASTDPDEVPDWLVIGFALPL-LPPSQDTGLTPDETALMAEGCAEVDPGGLIESWARHSLNWIARWEDEGTKPLHAEWRGL-ARNMGEDVT-Q
    ZP_01735773
    CGGVRFAADVSDPKARPKWLVIGIHVAF-KALNDEPGKNPNETCLQEEGCVEITPMALLESWSKHTLLWLTHFMDSGFERVHKEWRPR-CDTLGETI--S
    ZP_00959145
    CGGLRAMAASDDPEATPDWLVIGLTVPI-LPPSEDTGHAPDDTALLSEGCAEVDPPALLEAWARHTLSWLTRWEEDGPRALHAEWRGL-AHGIGEEIT-V
    ZP_01893656
    CGGVRFAADVSEPSAHPNWLVVGIDVPF-LPVGGEPGETPNQTCLHEEGCVEITPMALLESWSKHTLLWLTYYMDSGFERIHNEWRPR-CDTLGKMI--D
    ZP_01748741
    CGQMRAFASGTDPESVPDWLVIAWQLVL-LPLTEDTGTDPDRTALYAEGCADVDPGMLVEAWARHTLNWIAKWEDAGPRALAAEWRGL-AHGVGDETA-Q
    EDA78152
    CGYTFYQASTKFEEEIPEWLVLGINIPFLWSKSIESGNNPHKTVLSEEGCSDITPNILLESWSRHTLVWLNRFLDEGLLPIHNAWCEK-CEDVGKKI--T
    EDJ18898
    CGGMRAAAPTEDAEAEPDWLVIGIDVPF-RSETDAPGVTPDRTCLAEEGCIEITPERLLESFARHALVWINTWVEDGFAPLHEAWRGR-AWGLGEPLP--
    ECN28793
    CGRLRVAASHQKPEAAAEWLVVGLELPL-WPASDNPGETPDDTALYAEGCADVDALNLLESWVRHSLVWINRWQDEGVTPLHAEWRGL-AHGVGETTN-Q
    ZP_01749978
    CGALKVTAATTDPDEVPDWLIVGLTMPL-MAGTEDMGHTPDRTVLYAEGCADVAPSDLIEAWARHTLHWISRWEADGPRTLHTDWRGL-CHGIGEETG-V
    ECZ46228
    CGYTFYKAATKLEEEIPEWLVIGINIPFLWSKSTESGRLPEETVLFEEGCSEITPISLLESWSRHTLVWLNRFLDEGLLPVHNAWCEK-CENIGKKI--S
    ECW00844
    CGVLTCQASTTDPADIPNWLVIGVEIPFMRPAGLEPGENPESTWLYEEGCIELTVPQVIESWSRHALIWLRAFEDGGYAEIQSHWRAK-CDSIGQEI--E
    EBF28169
    CGRVSGAASTRDAAATPDWLVTGFDLTF-ARPDTQGGDTPDQTDLQSEGCGDLSPKQFLESWSRHLLNWINRWEEDGMAPLHREYAGL-VHGLGQEGQ-V
    ECZ95388 M
    GQVLLYSSDEELNEVPSWIVTGVQIRR-EVECLKFHETIEATSFEDEGASFLSNVRVIEAITRHFFVWLSTWQDKGFKPVYDTWMERIVPKFTVKEV-S
    Consensus/95% sG.h.h.tss......PpWllhthpl.b........G..Pp.T.L..EGC..l.s..llEtas+H.b.hls.a.......lb..W..b.s..hGp.....


    YP_612389 AG---RSGTFLGVDEDFGMLLRDE-T-TTHLIPLTTVLVQ
    ZP_01058811 NG---AS
    GTFLGVDEDFGMLLREA-D-TTRLIPLTTQL--
    ZP_01904194 SG---RT
    GTFLGVDENFGMLLRDD-T-KTHLIPLSSVL--
    ZP_01755469 QG---IE
    GSFLGLDENFNMLLRDG-E-TTHLIPLSSVL--
    ZP_01743189 KG---LK
    GTFLGIDERFGMLLRDE-T-DTHLIPLTHLLEE
    ZP_01035295 NG---LT
    GTFQGVDDRFGMLLRAE-D-TTHLIPLTTLL--
    ZP_01442737 DG---LT
    GKFLGVDEDFGMLLRDG-E-TTHLIPLTTVL--
    EDG76557 KD---SNAV
    FMGVDDNFGMLLRDD-DGTTSNIPLTTLLEE
    YP_167041 AN---CT
    GTFLGVDEKFGMLIRTG-A-DTRLIPLTALL--
    ZP_00948748 GD---LT
    GDFTGIDENFGLLLKTD-T-TTHLIPLTDLL--
    ZP_01549178 DG---TS
    GTFVGVDENFGMLLRTD-E-DTVLIPLSS----
    YP_683117 HG---LT
    GVFKGVDEDFGMILQSD-D-DTRIIPITDILTE
    EBF52230 SG---LH
    GTFLGVDENFGMLVRDS-N-TTHLIPLTTLL--
    ZP_01735773 YP---KP
    GVFFGLDEKGRMLLRQD-V-MTETLSL------
    ZP_00959145 TD(5)QT
    GTFLGTDEAFGLLLRQG-E-TTSLIPLTTLL--
    ZP_01893656 LP---KP
    GLFVGLDEKGRMLLRQD-V-MTETVSL------
    ZP_01748741 DG---RT
    GTFLGVDEDFGMLLRDA-D-GTHLIPLTTLL--
    EDA78152 YP---KQ
    GEFIGLDENGNMLLKNS-N-NT-----------
    EDJ18898 -----EG
    GVFMGLDEWGAQLVKHP-D-RTELRPLTRLL--
    ECN28793 NG---HN
    GKFLGTDERFGMLLRSA-E-TTHLIPLSTLL--
    ZP_01749978 SD---LT
    GTFVGVDEDFGMLLRDADD-TTHLIPLTTLL--
    ECZ46228 YP---KN
    GDFIGLDENGNMLLKKS-N-D------------
    ECW00844 AP---AS
    GIFVGTTETGGLLLRHN-G-LTDIYELTGQL-V
    EBF28169 LG---RT
    GHLLGLDEDLGLLLRSE-G-RTTVLPVTLLL--
    ECZ95388 EE---FK
    GTWIGLDENGLGLFKNN-K-DHFSLSLND-I--
    Consensus/95% .......G.a.GhD-.h.bLl+p.....p...........



    Superposition  between  protein structure of YP_612389.1 (cartoon representation) and biotin protein ligase (blue ribbon, PDB code 1wnl). Please note, the position of (non-conserved) Arg102 in YP_612389.1 (cyan stick) is similar to that of catalytic Lys111 of biotin protein ligase (blue stick; PDB code 1wnl; Bagautdinov et al. 2005):

          



    Ligand Summary



    References

    Reviews

    References

     

    No references found.

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