effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 137 LFAHLDDNERSDIFDAMFPVTHIAGETVIQQGNEGDNFYVVDQGEVDVYVNGE-----WVTNISEGGSFGELALIYGTPR 211
Cdd:cd00038     1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgreqIVGFLGPGDLFGELALLGNGPR 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462615328 212 AATVKAKTDLKLWGIDRDSYRRILMGSTLRKRKMY 246
Cdd:cd00038    81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 137 LFAHLDDNERSDIFDAMFPVTHIAGETVIQQGNEGDNFYVVDQGEVDVYVNGE-----WVTNISEGGSFGELALIYGTPR 211
Cdd:cd00038     1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgreqIVGFLGPGDLFGELALLGNGPR 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462615328 212 AATVKAKTDLKLWGIDRDSYRRILMGSTLRKRKMY 246
Cdd:cd00038    81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 160 AGETVIQQGNEGDNFYVVDQGEVDVYV---NGEWVT--NISEGGSFGELALIYGTPRAATVKAKTDLKLWGIDRDSYRRI 234
Cdd:pfam00027   6 AGEVIFREGDPADSLYIVLSGKVKVYRtleDGREQIlaVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPREDFLEL 85

                  ..
gi 2462615328 235 LM 236
Cdd:pfam00027  86 LE 87

Regulatory subunit of type II PKA R-subunit;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2462615328  25 HGIQQVLKDCIVHLCISKPERPMKFLREHFEKLEKEE 61
Cdd:pfam02197   1 HGLQALLEDLTVEVLRAQPSDPLQFAADYFEKLEEER 37

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462615328 255 ILESLEKWERLTVADALEPVQFEDGEKIVVQGEPGDDFYIITE 297
Cdd:cd00038     1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLS 43

bacteriocin-type transport-associated protein; Members of this protein family are uncharacterized and contain two copies of the cyclic nucleotide-binding domain pfam00027. Members are restricted to select cyanobacteria but are found regularly in association with a transport operon that, in turn, is associated with the production of putative bacteriocins. The models describing the transport operon are TIGR03794, TIGR03796, and TIGR03797.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 136 VLFAHLDDNERSDIFDAMFPVTHIAGETVIQQGNEGDNFYVVDQGE--VDVYVNGEW--VTNISEGGSFGELALIYGT-P 210
Cdd:TIGR03896 144 FIFGELHESDVAWMMASGTPQKLPAGTILIHEGGTVDALYILLYGEasLSISPDGPGreVGSSRRGEILGETPFLNGSlP 223

                          90       100
                  ....*....|....*....|....*
gi 2462615328 211 RAATVKAKTDLKLWGIDRDSYRRIL 235
Cdd:TIGR03896 224 GTATVKAIENSVLLAIDKQQLAAKL 248

cAMP-activated global transcriptional regulator CRP;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 163 TVIQQGNEGDNFYVVDQGEVDVYVNGE-----WVTNISEGGSFGELAL-IYGTPRAATVKAKTDLKLWGIDRDSYR---- 232
Cdd:PRK11753   30 TLIHAGEKAETLYYIVKGSVAVLIKDEegkemILSYLNQGDFIGELGLfEEGQERSAWVRAKTACEVAEISYKKFRqliq 109

                          90
                  ....*....|....*.
gi 2462615328 233 ---RILM--GSTLRKR 243
Cdd:PRK11753  110 vnpDILMalSAQMARR 125

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 137 LFAHLDDNERSDIFDAMFPVTHIAGETVIQQGNEGDNFYVVDQGEVDVYVNGE-----WVTNISEGGSFGELALIYGTPR 211
Cdd:cd00038     1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLSGSVEVYKLDEdgreqIVGFLGPGDLFGELALLGNGPR 80

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462615328 212 AATVKAKTDLKLWGIDRDSYRRILMGSTLRKRKMY 246
Cdd:cd00038    81 SATVRALTDSELLVLPRSDFRRLLQEYPELARRLL 115

dimerization/docking (D/D) domain of the Type I Regulatory subunit of cAMP-dependent protein kinase; cAMP-dependent protein kinase (PKA) is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of regulatory (R) subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. RI subunits are pseudo-substrates as they do not contain a phosphorylation site in their inhibitory site unlike RII subunits. RIalpha function is required for normal development as its deletion is embryonically lethal. RIbeta is expressed highly in the brain and is associated with hippocampal function. The R subunit contains an N-terminal dimerization/docking (D/D) domain, a linker with an inhibitory sequence, and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. PKA is present ubiquitously in cells and interacts with many different downstream targets. It plays a role in the regulation of diverse processes such as growth, development, memory, metabolism, gene expression, immunity, and lipolysis.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2462615328  15 LKGCELYVQLHGIQQVLKDCIVHLCISKPERPMKFLREHFEKLEKEENR 63
Cdd:cd12097     1 LKECEAYIQKHNIQQLLKDCIVQLCVDRPDNPVAFLREYFEKLEKESTR 49

Cyclic nucleotide-binding domain; This domain sensor domain can bind cAMP, cGMP, c-di-GMP, oxygen and 2-oxoglutarate (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462615328 160 AGETVIQQGNEGDNFYVVDQGEVDVYV---NGEWVT--NISEGGSFGELALIYGTPRAATVKAKTDLKLWGIDRDSYRRI 234
Cdd:pfam00027   6 AGEVIFREGDPADSLYIVLSGKVKVYRtleDGREQIlaVLGPGDFFGELALLGGEPRSATVVALTDSELLVIPREDFLEL 85

                  ..
gi 2462615328 235 LM 236
Cdd:pfam00027  86 LE 87

Regulatory subunit of type II PKA R-subunit;

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 2462615328  25 HGIQQVLKDCIVHLCISKPERPMKFLREHFEKLEKEE 61
Cdd:pfam02197   1 HGLQALLEDLTVEVLRAQPSDPLQFAADYFEKLEEER 37

effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. Cyclic nucleotide-binding domain similar to CAP are also present in cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) and vertebrate cyclic nucleotide-gated ion-channels. Cyclic nucleotide-monophosphate binding domain; proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues; the best studied is the prokaryotic catabolite gene activator, CAP, where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure; three conserved glycine residues are thought to be essential for maintenance of the structural integrity of the beta-barrel; CooA is a homodimeric transcription factor that belongs to CAP family; cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain; cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain; cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section; also found in vertebrate cyclic nucleotide-gated ion-channels

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462615328 255 ILESLEKWERLTVADALEPVQFEDGEKIVVQGEPGDDFYIITE 297
Cdd:cd00038     1 LFSGLDDEELEELADALEERRFPAGEVIIRQGDPADSLYIVLS 43

dimerization/docking (D/D) domain found in the testis-specific expressed protein 55 (TEX55)-like family; The TEX55-like family includes TEX55, F-box/LRR-repeat protein 13 (FBXL13), adenylate kinase isoenzymes AK5 and AK8, as well as uncharacterized EF-hand calcium-binding domain-containing protein 10 (EFCAB10), and protein VEST-1. TEX55, also called testis-specific conserved cAMP-dependent type II PK-anchoring protein (TSCPA), is a putative A-kinase anchoring protein (AKAP) that is dispensable for male fertility. FBXL13, also called F-box and leucine-rich repeat protein 13, or dynein regulatory complex subunit 6 (DRC6), is a component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule sliding in motile axonemes. It may also function as a substrate-recognition component of an SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex. AK5 and AK8 act as nucleoside monophosphate (NMP) kinases that catalyze the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. Members of this family contain a conserved helical bundle domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2462615328  15 LKGCELYVQLHGIQQVLKDCIVHLCISKPERPMKFLREHFEKL 57
Cdd:cd22961     1 LEDAEEYLEKHKIPELFESLLTALLIEKPEDPIEFLIDKLQQI 43

dimerization/docking (D/D) domain found in EF-hand calcium-binding domain-containing protein 10 (EFCAB10) and similar proteins; The subfamily includes uncharacterized EF-hand calcium-binding domain-containing protein 10 (EFCAB10), which contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 2462615328  19 ELYVQLHGIQQVLKDCIVHLCISKPERPMKFLREHFEKL 57
Cdd:cd22976     5 EEYLEKHKIPELFENLTSLLLYHRPEDPKAFLIEQLEKL 43

dimerization/docking (D/D) domain found in Trypanosoma brucei adenylate kinase (AK) and similar proteins; AK (EC 2.7.4.3), also called ATP-AMP transphosphorylase, ATP:AMP phosphotransferase, or adenylate monophosphate kinase, catalyzes the reversible transfer of the terminal phosphate group between ATP and AMP. It plays an important role in cellular energy homeostasis and in adenine nucleotide metabolism. Members of this subfamily contain an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 2462615328  21 YVQLHGIQQVLKDCIVHLCISKPERPMKFLREHFEK 56
Cdd:cd22981     8 YLKEKNIPQLFEFLLRHLLLDKPENPLEYLHDLLER 43

dimerization/docking (D/D) domain found in adenylate kinase isoenzyme 8 (AK8) and similar proteins; AK8 (EC 2.7.4.3/EC 2.7.4.6), also called ATP-AMP transphosphorylase 8, acts as a nucleoside monophosphate (NMP) kinase that catalyzes the reversible transfer of the terminal phosphate group between nucleoside triphosphates and monophosphates. It has highest activity toward AMP, and weaker activity toward dAMP, CMP and dCMP. It also displays broad nucleoside diphosphate kinase activity. AK8 contains an N-terminal domain that shows high sequence similarity to the dimerization/docking (D/D) domains of regulatory subunit of cAMP-dependent protein kinase (PKA) and protein DPY-30/SDC1.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2462615328  19 ELYVQLHGIQQVLKDCIVHLCISKPERPMKFLREHFEK 56
Cdd:cd22979     7 AAYAEKHRIFELFQDLLKQLLIHKPEDPLQFLIDYLQK 44

dimerization/docking (D/D) domains found in the cAMP-dependent protein kinase regulatory subunit (PRKAR) and the DPY30/SDC1-like family; This hierarchy includes the dimerization/docking (D/D) domains of type I and type II cAMP-dependent protein kinase (PKA) regulatory (R) subunits, DPY30 from animals and its homologs, SDC1 from yeasts, and similar domains. PKA is a serine/threonine kinase (STK), catalyzing the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. The inactive PKA holoenzyme is a heterotetramer composed of two phosphorylated and active catalytic subunits with a dimer of R subunits. Activation is achieved through the binding of the important second messenger cAMP to the R subunits, which leads to the dissociation of PKA into the R dimer and two active subunits. There are two classes of R subunits, RI and RII; each exists as two isoforms (alpha and beta) from distinct genes. These functionally non-redundant R isoforms allow for specificity in PKA signaling. The R subunit contains an N-terminal D/D domain, a linker with an inhibitory sequence (IS), and two c-AMP binding domains. The D/D domain dimerizes to form a four-helix bundle that serves as a docking site for A-kinase-anchoring proteins (AKAPs), which facilitates the localization of PKA to specific sites in the cell. DPY30, also called dumpy-30, was initially discovered in Caenorhabditis elegans as a key player in X chromosome dosage compensation. Human DPY30 plays a dual function in moderately regulating the methyltransferase activity of SET1/COMPASS (COMplex of Proteins ASsociated with Set1) enzymes and contributing to the recruitment of the complex to chromatin. Yeast SDC1 (suppressor of CDC25 protein 1) is the smallest subunit of COMPASS (COMplex of Proteins ASsociated with Set1) and interacts exclusively with Bre2 at the distal end of the catalytic module. It positively regulates the COMPASS catalytic module by stabilizing the non-canonical Bre2 SPRY domain. DPY30/SDC1 contains a C-terminal helical bundle domain that directly interacts with Ash2L (in human)/Bre2 (in yeast) COMPASS through the DPY30-binding motif (DBM). The DPY30/SDC1 helical bundle domain, also called D/D domain, is formed of two alpha-helices that may be analogous to the D/D domain found in regulatory subunit of PKA.

                          10        20
                  ....*....|....*....|....*...
gi 2462615328  30 VLKDCIVHLCISKPERPMKFLREHFEKL 57
Cdd:cd22957     2 LLQDAVAKLLEERPEDPVEFLAEYFEKA 29