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: 17-Jan-2013
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:
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1             ##                                                                        
1D3Y_B      123 DFILAIETSGMFARLNAErfwd----------------khncILVSLKGVPARATRRFIKRLHEeh-------dlPVLVF 179
gi 3025217  196 DFILVVEKDTTFQKLMDEnfqam---------------fprgILATSKGYPDIATRNVLKMLSEkr-------kfPIYGL 253
gi 19074189 138 KKTVVVEKDTVLQRIASEierek--------------cleeiLFVCGKGYPCKNTVLLLKMIEHk---------tAVAGL 194
gi 74834166 163 KWILVVEKETVYFHLINEmhqef---------------lqntVLITGKGYPCYATKSFVKYLSImnp------yiPVYYF 221
gi 29249284 166 QFVLVIEKDTVFEHLIDSyeaikd------------rlgqsfMVITGKGYPDAATRALVSFLDScr--------iPIFGL 225
gi 49642842 226 LKVIVLEKDAIFQQLIQCqemi-----------------kdwIIVTGKGYPDHLSRELLHKLDLslq-----gnvQFHIF 283
gi 39576479 201 DFCLIVESEGTANTLVTMgftk----------------rnncIVMGAQGVPSNGVRGWAKLIQEel-------dvPMYFF 257
gi 55244408 113 KLVLVVEKDTVFKRLLEDgilst--------------fpdtlVLITAKGYPDVSTRLLLKKISDwt-------hvPIYGL 171
gi 50556168 166 NCILIVEKEAVFTTLCAYipk-------------------dtLLITGKGYPDHMTQDFVRLFDEm---------lPLFIC 217
gi 83589355 258 PWVLLVENLTSYYQVVQSvselavpcreggggrglavegpagLVVYTGGFPHRGVQLFLRRLQDyrespgatarpPVYHW 337
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        # #      #                                                                     
1D3Y_B      180 TDGDPYGyLNIYRTLKV----GSGKAIHLADkls---ipAARLIGVtpqdiid----------ydlpthPLKEQDIKRIK 242
gi 3025217  254 FDADPHG-IEIYLTYKY----GPTKEFAEGRgaf---vpTIEWIGLfptdfhrf-------tidqsqclPLVRTDFVKIE 318
gi 19074189 195 FDLDPFG-IHIFCIYKY----GSKETPDIRVe-------TIMRIGVcmedvlek-------naykdvfvKLNVHDLKMIN 255
gi 74834166 222 GDMDPHG-YDILQQYAF----GNAYTSHELN--------NIPWIQWlnsyfpld-------qlqikkknKLNQRELQLLE 281
gi 29249284 226 ADGDAHG-MNILCTYAY----GSASATRKSVvpnhyiapSLVPIGVfnshiqrsskaikgsrhcdpadlKLYDILITRLT 300
gi 49642842 284 TDSDPYG-IDIVTKYMV----KCPRLIHKGVll----nqLITRNTEsnsm---------------lvllPLSLRDATFAM 339
gi 39576479 258 GDLDAYTmQNIFRTLKA----GSAASLIRNAdfs---apNVKFLGVlpedvkkydl----phykvkesdPAEARALKKAK 326
gi 55244408 172 MDADPHG-IEIFCVYKF----GSLAMVHQQRsla---vpTMRWIGLfpsdiel----------lglqgvPLREGELKRIE 233
gi 50556168 218 VDADPHG-IHIAATYRYrsfvRAPSLQGLGS--------SISYIGVslvdf-------------krghlPLEDKNRKHAG 275
gi 83589355 338 GDMDYGG-IRICEYIRRn--lIPDLQPYLMDvtt---ytRYLPAGIpf--------------------gDEYAARLRHLA 391
                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|..
Feature 1                                                           
1D3Y_B      243 DGLknddfv-----------rsfpeWQKALKQMLDMGVRAEQQSLAKYGLKY 283
gi 3025217  319 KMIprsiq------------lgeivVTRELDWMIQNKFKMELESINMCGQEY 358
gi 19074189 256 RLVrf------------------geLSADLLFLRKIDGKVEMEALFSKEPRR 289
gi 74834166 282 QIKsn------------------anLPEEWKQIMDNKEKYEIEDMQFQNLSE 315
gi 29249284 301 ALGrl-------------------eWANEVQNLAALGMQYELETILGQEGGL 333
gi 49642842 340 GLIrrlckeeeeeegsvrkhtmrqnLKYEVQRQLFFQRKGEMNVVNNGNVQQ 391
gi 39576479 327 DALendpffl---------dkknknLADILRWLIKEKIRCEQQSFFSVDPKD 369
gi 55244408 234 QMTkrpy--------------teghIQRELLLLRQLATKVEIESLYNIASDF 271
gi 50556168 276 RLLsaitgrqaeal-elgdyiemnkWKLELQRMLFLGKVAEMNVAGDGSEGR 326
gi 83589355 392 EDPay------------------apWHPLLQAMLKHRKWVEQESIAINVSWA 425

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