1VJ7,2BE3,1VJ7


Conserved Protein Domain Family
NT_Rel-Spo_like

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cd05399: NT_Rel-Spo_like 
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Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases.
This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydrolase domain (TGS). Some Rel-Spo proteins also have a C-terminal regulatory ACT domain. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition.Two of the three catalytic carboxylates are found in Rel-Spo enzymes, with the second carboxylate of the DXD motif missing. Evidence supports a single-cation synthetase mechanism.
Statistics
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PSSM-Id: 143389
View PSSM: cd05399
Aligned: 92 rows
Threshold Bit Score: 55.0459
Threshold Setting Gi: 17549593
Created: 18-May-2007
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:synthetase active site [active site]
Evidence:
  • Comment:For Streptococcus equisimilis SeqRel, a reciprocal regulatory mechanism ensures that the opposing activities, (p)ppGpp synthesis and degradation, located in two domains within the same monomer, are not co-induced.
  • Structure:1VJ7_A, Streptococcus equisimilis, bifunctional catalytic fragment of Relseq monomer, showing the synthetase active site bound with GDP, (hydrolase-OFF/synthetase-ON), contacts determined at 4A.
    View structure with Cn3D
  • Comment:The VJ7 structure contains two monomers, one in the hydrolase-OFF/synthetase-ON state, the other in the hydrolase-ON/synthetase-OFF state.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                       # #                               
1VJ7_A        215 EALVDDIVTKIKSYtteq--------------------glfGDVYGRPKHIYSIYRKMRDKKkrf-----------dqIF 263  Streptococcus...
XP_384798     112 QALNQYLTHQLEESsi------------------------rATLHSRVKKDDSISKSIDRREehwgktydspkqildgIH 167  Gibberella ze...
NP_719378      76 HAAQHELGNLLQKItth---------------------sqtHAILPEVKSYQRAAEKVASKFngd----------asqIT 124  Shewanella on...
YP_001279480  220 KYQKETIQQYLNYVld------------------------kHHISGHVRVLENQVIMYRQFFrnr-----------geID 264  Psychrobacter...
ZP_01064172   128 KDIKNEFGKEYSEIspvlnslqlttsdlinkklhfirnelaFEPQIRVKSWDSTVDKLARLNsrfe--------klteLQ 199  Vibrio sp. ME...
CAD16898     1974 HAASARITSLLQANlhgwagp-------------gagavrlAGLKHAVKSAGSLEDKLGYLIagkqldl---peavsqVN 2037 Ralstonia sol...
NP_644512    2456 RQMEPQLTDMLQNIagrh-------------------ggqlAGTQHQLKSYSSLQEKLMQRVvlkkqsl---eeaaagVN 2513 Xanthomonas a...
NP_522933    2032 EAQLRHCARTLHAAarlvepeitpv-----ikaaiegigalRGQAHRVKTERALHDKLRVLLhrghpsp---adaaamVN 2103 Ralstonia sol...
AAP13893       70 QRAERSISPMVRAAaris-------------------datvVGFDHRLKSPDSLKRKVATSLketpget--adqalarIN 128  Streptomyces ...
ZP_01689570   246 DTQLLEVQKLLSKGhr-----------------------kvTAHKSDIKGWDRAYDKQQNKYrda-----------slIK 291  Microscilla m...
Feature 1         ##   #                                # #             # #   #   #               
1VJ7_A        264 DLIAIRCVMet---qsDVYAMVGYIHe--LWRPmpgRFKDYIAa---------PKAN--GYQSIHTTVYGPk-------- 319  Streptococcus...
XP_384798     168 DLLGFRIVVdy---psGLDQSYQLIKk--HFSV---ERINTFStdrdvgvlwkPRFG--AYEGKNFQVRMSpdehnvgls 237  Gibberella ze...
NP_719378     125 DLARASIVAd-----sISELMQAYYTlseQTQVv--KLKNRFAe---------PKAS--GYRDLNLLVRLPes------- 179  Shewanella on...
YP_001279480  265 DLLRHYAFEivtttieDCDLLADYLIk--KYRIadrYVEDNIRh---------PLPG--GNQSLTLTYKRDn-------- 323  Psychrobacter...
ZP_01064172   200 DLLGVRVVTif---esDLLEVEKVIGk--SFSVvkrYRPEYIA----------NKES--NAKHIIIKLKNSetk------ 256  Vibrio sp. ME...
CAD16898     2038 DALRYSIVLpsptfvpASRRILAGLE---EHGHamtERTNHFA----------RRGS--AFRALSVTLRDPsd------- 2095 Ralstonia sol...
NP_644512    2514 DALRYSVVLepqdftaGLRAVLAALDdrgHARV---KLTNQFT----------AYPP--SFKAINVTLRSPa-------- 2570 Xanthomonas a...
NP_522933    2104 DALRYSVVLkpddfaaGYAEVLGNLDragLIKT---RVHNAFK----------PAWD--PFKGINVKFMGRdaa------ 2162 Ralstonia sol...
AAP13893      129 DSVRYTLQWpdgryvhGVALASSVLA---AWGNd--SVKWSNTw--------gRKQGykAVNSAWRDPLEG--------- 186  Streptomyces ...
ZP_01689570   292 DLVRGTLVFns---vtDLVQGRDYIYq--CFTVy--GTKNSIGh---------PTET--GYQDMKINVKLSt-------- 345  Microscilla m...
Feature 1                # # #       ## 
1VJ7_A        320 ----GPIEIQIRTKEMHQVAEY 337  Streptococcus dysgalactiae subsp. equisimilis
XP_384798     238 iyyeVLFEIQVTSIAESLYNRL 259  Gibberella zeae PH-1
NP_719378     180 ---gMIAEVQLHLKEIADIKSG 198  Shewanella oneidensis MR-1
YP_001279480  324 ----DIIKVTLLTRKMQAVSRL 341  Psychrobacter sp. PRwf-1
ZP_01064172   257 --dqVIAEVQIMTLSQFLLNRV 276  Vibrio sp. MED222
CAD16898     2096 ---gLLWEVQFHTEQTFELKER 2114 Ralstonia solanacearum GMI1000
NP_644512    2571 ---gALWEIQFHTPETFALKER 2589 Xanthomonas axonopodis pv. citri str. 306
NP_522933    2163 -gqsVRLEVQFHTDETFALKMR 2183 Ralstonia solanacearum GMI1000
AAP13893      187 ----HVFEVQFHTPQSKWAQEA 204  Streptomyces morookaensis
ZP_01689570   346 ---gHIGELQLHLQSMVESKHA 364  Microscilla marina ATCC 23134

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