Conserved Protein Domain Family
TopoII_MutL_Trans

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cd00329: TopoII_MutL_Trans 
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MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families.
Statistics
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PSSM-Id: 73195
View PSSM: cd00329
Aligned: 294 rows
Threshold Bit Score: -1
Threshold Setting Gi: 0
Created: 6-Mar-2002
Updated: 9-Mar-2011
Structure
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Program:
Drawing:
Aligned Rows:
Hierarchy
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ATP binding
Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:ATP binding site [chemical binding site]
Evidence:
  • Structure:1B63_A, Escherichia coli MutL bound with Adpnp ((non-hydrolyzable ATP analog), contacts at 3.5A
    View structure with Cn3D
  • Structure:1EI1_A, E. Coli Dna Gyrase B dimer bound with ADPNP (non-hydrolyzable ATP imido analog), contacts at 3.5A
    View structure with Cn3D
  • Structure:1QZR_B, Saccharomyces cerevisiae, topo IIA dimer bound to ADPNP, contacts at 3.5 A
    View structure with Cn3D
  • Structure:1Z5C_B, Sulfolobus shibatae Topo Vi-B dimer, ADP contacts at 3.5A
    View structure with Cn3D
  • Comment:conserved Lys residue from the transducer domain interacts with the gamma-phosphate of bound nucleotide.

cd00329 is part of a hierarchy of related CD models.
Use the graphical representation to navigate this hierarchy.
cd00329:TopoII_MutL_Transcd00782:MutL_Transcd00822:TopoII_Trans_DNA_gyrasecd00823:TopoIIB_Transcd03481:TopoIIA_Trans_ScTopoIIAcd03482:MutL_Trans_MutLcd03483:MutL_Trans_MLH1cd03484:MutL_Trans_hPMS_2_likecd03485:MutL_Trans_hPMS_1_likecd03486:MutL_Trans_MLH31EI1 A72254333772471766475311402507871062265247537677626151084363306379565161KIJ A6458625718514825402011746222712044853343961002856617723465987719162654843113410640369681595716820923018145733138785246793232973659676199154571058045218143663121887391572521648310133588223323612647443534482175403339868315593244626186156434171344045678375130680397170809313812265664753319713409683536032350907726454108689946052946413527164745855014089786707048923914289867404663128305398599014021778386079013638361847871045800212468245812324437688375711467546376718471177226935563118198471411645644630566038252611001534540199463996253914288332365841QZR B851074441ZXN D453821612827729956269784135995720077956175065572228371264410511747405091180740804954463705968336716666826863190687544637059472428822463847866814704408049523069217870831119274472122419827467917263776845921Z5C B1MX0 A138141501831318713124626262210813124830131246013122957131246111991546040068663861592627148308612331188531248952009435739576480472302024911541362003157507485007200710766810333496554304952874550305373449800776325093502584001EA6 B5313374072010834665323465524572885108983509100052645062550259094710069464952725544984090134673750305491496524696849102823498929170968450552768564672816835047238768426635825470905750708317891709683282772705313065833416431472220347204155042545788369529385111036675222146323063495242224498475466519023204551648928214156392953521184322296193866072305668728167920569204555037249528820455106170918820139217204551304887111758254063425185626251442728271720230234436805608676556785553792047300285073292472078533410549345523447131928771911299185108177505483933893081349057647102224965305021235083755025784244984209503070534952561149658171170905668560962779963297154156457224502762584647768405882500772767963678358996267849238181448172045512027262202463994146820869989282188928240200894116821137458002119776905355655125020455124564165964241011372393988518565758585979186158140324456251B63 A78701445768741477688218156178452857107586915817452630014113869262790438578363714295416573356669720455160301807396821370249531441566041207431753571848398475753636791082420455088344967972045515248854181345402358613171483755631216480596792654962257382419472139983989718398627754499115642797715475334657889978220908682467011EI1 A72254333772471766475311402507871062265247537677626151084363306379565161KIJ A6458625718514825402011746222712044853343961002856617723465987719162654843113410640369681595716820923018145733138785246793232973659676199154571058045218143663121887391572521648310133588223323612647443534482175403339868315593244626186156434171344045678375130680397170809313812265664753319713409683536032350907726454108689946052946413527164745855014089786707048923914289867404663128305398599014021778386079013638361847871045800212468245812324437688375711467546376718471177226935563118198471411645644630566038252611001534540199463996253914288332365841QZR B851074441ZXN D453821612827729956269784135995720077956175065572228371264410511747405091180740804954463705968336716666826863190687544637059472428822463847866814704408049523069217870831119274472122419827467917263776845921Z5C B1MX0 A138141501831318713124626262210813124830131246013122957131246111991546040068663861592627148308612331188531248952009435739576480472302024911541362003157507485007200710766810333496554304952874550305373449800776325093502584001EA6 B5313374072010834665323465524572885108983509100052645062550259094710069464952725544984090134673750305491496524696849102823498929170968450552768564672816835047238768426635825470905750708317891709683282772705313065833416431472220347204155042545788369529385111036675222146323063495242224498475466519023204551648928214156392953521184322296193866072305668728167920569204555037249528820455106170918820139217204551304887111758254063425185626251442728271720230234436805608676556785553792047300285073292472078533410549345523447131928771911299185108177505483933893081349057647102224965305021235083755025784244984209503070534952561149658171170905668560962779963297154156457224502762584647768405882500772767963678358996267849238181448172045512027262202463994146820869989282188928240200894116821137458002119776905355655125020455124564165964241011372393988518565758585979186158140324456251B63 A7870144576874147768821815617845285710758691581745263001411386926279043857836371429541657335666972045516030180739682137024953144156604120743175357184839847575363679108242045508834496797204551524885418134540235861317148375563121648059679265496225738241947213998398971839862775449911564279771547533465788997822090868246701
cd00329 Sequence Cluster
cd00329 Sequence Cluster
Sub-family Hierarchy
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CD Hierarchy
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:

Feature 1                                                                                      
1EI1_A      221 IKAFVEYLN.[9].IFYFS.[ 7].VEVALQ.[ 7].NIYCFTNNIPQ.[3].GTHLAGFRA.[31].LIAVVSVKVPD 328
1B63_A      210 KERRLGAIC.[7].ALAIE.[ 7].LRGWVA.[11].IQYCYVNGRMM.[2].RLINHAIRQ.[11].PAFVLYLEIDP 298
gi 12331188 411 LRLGIIKEL.[4].VATYS.[12].VEAGVS.[10].NIFRFANRIPL.[7].VVTRTALKR.[14].IGVFVSIVSTK 508
gi 13124601 367 IKRGLTGIL.[4].VTAVT.[13].VEVGLA.[ 8].EILRYANRVPL.[6].CVITSAVRS.[15].LVVLVNVISVH 463
gi 13124611 518 LEAGLRTEF.[4].YAAAT.[12].VEAGIA.[11].QLMRFANRVPL.[6].CATTDVLGD.[20].AVIMVHVASTN 621
gi 19915460 325 IYRGLEKET.[4].IATST.[12].VEVGLA.[11].SIMRFANRVPL.[6].CVTTHAVED.[19].VLLLIHVASIN 427
gi 39576480 324 LSKSITRLG.[4].FAVVT.[12].VEVALA.[13].TLLRFANRVPL.[6].CAITWAIES.[19].YIFAVSIVSPF 428
gi 40068663 329 LQIGITKEY.[4].LAVKT.[13].VEVAIG.[ 7].EILRFANRTPL.[6].CAIVKAIKD.[17].ALILVHIASVK 426
gi 53124895 438 LRLGIIKEL.[4].VATHA.[12].VEAGIS.[10].NIFRYANRIPL.[7].VITRTALKR.[14].IGVFVSIVSTK 535
gi 71483086 322 IKKGLKNVL.[8].AQPIT.[12].VEAGIV.[11].RILRFANRVPL.[6].DVITKAISS.[20].AIILVHVASTR 429

Feature 1                        #    
1EI1_A      329      PKFS     SQTKDKLV 340
1B63_A      299 .[2].VDVN.[1].HPAKHEVR 313
gi 12331188 509      IPFK     GTGKEYIG 520
gi 13124601 464      VPYT     STGKQSIA 475
gi 13124611 622      VPFT     SESKDAIA 633
gi 19915460 428      VPFT     SESKDAIA 439
gi 39576480 429      IKFK     NASKETID 440
gi 40068663 427      VPYT     SESKEAIA 438
gi 53124895 536      IPFK     GTGKEYIG 547
gi 71483086 430      VPFT     SEAKEAIA 441

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