1D3Y


Conserved Protein Domain Family
TOPRIM_TopoIIB_SPO

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cd00223: TOPRIM_TopoIIB_SPO 
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TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. 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. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD. For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Statistics
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PSSM-Id: 173774
View PSSM: cd00223
Aligned: 51 rows
Threshold Bit Score: 104.644
Threshold Setting Gi: 68205494
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1           ##                                                                        
1D3Y_B    123 DFILAIETSGMFARLNAErfwd----------------khncILVSLKGVPARATRRFIKRLHEeh-------dlPVLVF 179 Methanocaldococcus...
Q22236    196 DFILVVEKDTTFQKLMDEnfqam---------------fprgILATSKGYPDIATRNVLKMLSEkr-------kfPIYGL 253 Caenorhabditis ele...
NP_584795 138 KKTVVVEKDTVLQRIASEierek--------------cleeiLFVCGKGYPCKNTVLLLKMIEHk---------tAVAGL 194 Encephalitozoon cu...
CAI44467  163 KWILVVEKETVYFHLINEmhqef---------------lqntVLITGKGYPCYATKSFVKYLSImnp------yiPVYYF 221 Paramecium tetraur...
EAA40799  166 QFVLVIEKDTVFEHLIDSyeaikd------------rlgqsfMVITGKGYPDAATRALVSFLDScr--------iPIFGL 225 Giardia lamblia AT...
CAH00804  226 LKVIVLEKDAIFQQLIQCqemi-----------------kdwIIVTGKGYPDHLSRELLHKLDLslq-----gnvQFHIF 283 Kluyveromyces lact...
CAE80644  201 DFCLIVESEGTANTLVTMgftk----------------rnncIVMGAQGVPSNGVRGWAKLIQEel-------dvPMYFF 257 Bdellovibrio bacte...
EAA05541  113 KLVLVVEKDTVFKRLLEDgilst--------------fpdtlVLITAKGYPDVSTRLLLKKISDwt-------hvPIYGL 171 Anopheles gambiae ...
XP_505492 166 NCILIVEKEAVFTTLCAYipk-------------------dtLLITGKGYPDHMTQDFVRLFDEm---------lPLFIC 217 Yarrowia lipolytic...
YP_429364 258 PWVLLVENLTSYYQVVQSvselavpcreggggrglavegpagLVVYTGGFPHRGVQLFLRRLQDyrespgatarpPVYHW 337 Moorella thermoace...
Feature 1      # #      #                                                                     
1D3Y_B    180 TDGDPYGyLNIYRTLKV----GSGKAIHLADkls---ipAARLIGVtpqdiid----------ydlpthPLKEQDIKRIK 242 Methanocaldococcus...
Q22236    254 FDADPHG-IEIYLTYKY----GPTKEFAEGRgaf---vpTIEWIGLfptdfhrf-------tidqsqclPLVRTDFVKIE 318 Caenorhabditis ele...
NP_584795 195 FDLDPFG-IHIFCIYKY----GSKETPDIRVe-------TIMRIGVcmedvlek-------naykdvfvKLNVHDLKMIN 255 Encephalitozoon cu...
CAI44467  222 GDMDPHG-YDILQQYAF----GNAYTSHELN--------NIPWIQWlnsyfpld-------qlqikkknKLNQRELQLLE 281 Paramecium tetraur...
EAA40799  226 ADGDAHG-MNILCTYAY----GSASATRKSVvpnhyiapSLVPIGVfnshiqrsskaikgsrhcdpadlKLYDILITRLT 300 Giardia lamblia AT...
CAH00804  284 TDSDPYG-IDIVTKYMV----KCPRLIHKGVll----nqLITRNTEsnsm---------------lvllPLSLRDATFAM 339 Kluyveromyces lact...
CAE80644  258 GDLDAYTmQNIFRTLKA----GSAASLIRNAdfs---apNVKFLGVlpedvkkydl----phykvkesdPAEARALKKAK 326 Bdellovibrio bacte...
EAA05541  172 MDADPHG-IEIFCVYKF----GSLAMVHQQRsla---vpTMRWIGLfpsdiel----------lglqgvPLREGELKRIE 233 Anopheles gambiae ...
XP_505492 218 VDADPHG-IHIAATYRYrsfvRAPSLQGLGS--------SISYIGVslvdf-------------krghlPLEDKNRKHAG 275 Yarrowia lipolytic...
YP_429364 338 GDMDYGG-IRICEYIRRn--lIPDLQPYLMDvtt---ytRYLPAGIpf--------------------gDEYAARLRHLA 391 Moorella thermoace...
Feature 1                                                         
1D3Y_B    243 DGLknddfv-----------rsfpeWQKALKQMLDMGVRAEQQSLAKYGLKY 283 Methanocaldococcus jannaschii
Q22236    319 KMIprsiq------------lgeivVTRELDWMIQNKFKMELESINMCGQEY 358 Caenorhabditis elegans
NP_584795 256 RLVrf------------------geLSADLLFLRKIDGKVEMEALFSKEPRR 289 Encephalitozoon cuniculi GB-M1
CAI44467  282 QIKsn------------------anLPEEWKQIMDNKEKYEIEDMQFQNLSE 315 Paramecium tetraurelia
EAA40799  301 ALGrl-------------------eWANEVQNLAALGMQYELETILGQEGGL 333 Giardia lamblia ATCC 50803
CAH00804  340 GLIrrlckeeeeeegsvrkhtmrqnLKYEVQRQLFFQRKGEMNVVNNGNVQQ 391 Kluyveromyces lactis NRRL Y-1140
CAE80644  327 DALendpffl---------dkknknLADILRWLIKEKIRCEQQSFFSVDPKD 369 Bdellovibrio bacteriovorus HD100
EAA05541  234 QMTkrpy--------------teghIQRELLLLRQLATKVEIESLYNIASDF 271 Anopheles gambiae str. PEST
XP_505492 276 RLLsaitgrqaeal-elgdyiemnkWKLELQRMLFLGKVAEMNVAGDGSEGR 326 Yarrowia lipolytica CLIB122
YP_429364 392 EDPay------------------apWHPLLQAMLKHRKWVEQESIAINVSWA 425 Moorella thermoacetica ATCC 39073

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