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Conserved domains on  [gi|1820722648|ref|XP_032620357|]
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mitogen-activated protein kinase kinase kinase 2-like isoform X2 [Chelonoidis abingdonii]

Protein Classification

PB1_Mekk2_3 domain-containing protein( domain architecture ID 10157386)

PB1_Mekk2_3 domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PB1_Mekk2_3 cd06405
The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 ...
 52-129 6.65e-40

The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The MEKK2 and MEKK3 proteins contain a type II PB1 domain.


:

Pssm-ID: 99726  Cd Length: 79  Bit Score: 132.13  E-value: 6.65e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1820722648  52 VRVKFEHRGEKRILQFLRPVKLEDLASKAKVAFGQPMDLHYSNNELVIPLTTQDDLDKAVELLDRSVHMKSLKILLVI 129
Cdd:cd06405     1 VRIKFEHNGEKRIIQFPRPVKFKDLQQKVTTAFGQPMDLHYTNNELLIPLKNQEDLDRAIELLDRSPHMKSLRILLSA 78
RNAP_largest_subunit_C super family cl29012
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ...
 9-88 8.42e-03

Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.


The actual alignment was detected with superfamily member cd02737:

Pssm-ID: 355888 [Multi-domain]  Cd Length: 381  Bit Score: 37.02  E-value: 8.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648   9 SIEQQALNSIMQdlAVLHKASRPALPVQETGKPKSSSPKKQNDVRV-----------KFE-HRGEKRILQFLRPVKLEDL 76
Cdd:cd02737    11 AISEPAYKALLD--PPQSLESSPLELLKEVLECRSKSKSKENDRRVilslhlckcdhGFEyERAALEVKNHLERVTLEDL 88

                          90
                  ....*....|..
gi 1820722648  77 ASKAKVAFGQPM 88
Cdd:cd02737    89 ATTSMIKYSPQA 100
 
Name Accession Description Interval E-value
PB1_Mekk2_3 cd06405
The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 ...
 52-129 6.65e-40

The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The MEKK2 and MEKK3 proteins contain a type II PB1 domain.


Pssm-ID: 99726  Cd Length: 79  Bit Score: 132.13  E-value: 6.65e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1820722648  52 VRVKFEHRGEKRILQFLRPVKLEDLASKAKVAFGQPMDLHYSNNELVIPLTTQDDLDKAVELLDRSVHMKSLKILLVI 129
Cdd:cd06405     1 VRIKFEHNGEKRIIQFPRPVKFKDLQQKVTTAFGQPMDLHYTNNELLIPLKNQEDLDRAIELLDRSPHMKSLRILLSA 78
PB1 smart00666
PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. ...
 51-128 2.18e-13

PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.


Pssm-ID: 214770  Cd Length: 81  Bit Score: 63.38  E-value: 2.18e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648   51 DVRVKFEHRGEKRILQFLRPVKLEDLASKAKVAFG---QPMDLHYSNNEL-VIPLTTQDDLDKAVELLDRSvHMKSLKIL 126
Cdd:smart00666   1 TVDVKLRYGGETRRLSVPRDISFEDLRSKVAKRFGldnQSFTLKYQDEDGdLVSLTSDEDLEEAIEEYDSL-GSKKLRLH 79


                   ..
gi 1820722648  127 LV 128
Cdd:smart00666  80 VF 81
PB1 pfam00564
PB1 domain;
51-128 2.88e-12

PB1 domain;


Pssm-ID: 395447  Cd Length: 84  Bit Score: 60.77  E-value: 2.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648  51 DVRVKFEHRGEK-RILQFLRPVKLEDLASKAKVAFGQPM---DLHYSNNEL-VIPLTTQDDLDKAVELLDRSVhMKSLKI 125
Cdd:pfam00564   1 TVRLKLRYGGGIrRFLSVSRGISFEELRALVEQRFGLDDvdfKLKYPDEDGdLVSLTSDEDLEEALEEARSLG-SKSLRL 79


                  ...
gi 1820722648 126 LLV 128
Cdd:pfam00564  80 HVF 82
RNAP_IV_NRPD1_C cd02737
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
 9-88 8.42e-03

Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.


Pssm-ID: 132724 [Multi-domain]  Cd Length: 381  Bit Score: 37.02  E-value: 8.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648   9 SIEQQALNSIMQdlAVLHKASRPALPVQETGKPKSSSPKKQNDVRV-----------KFE-HRGEKRILQFLRPVKLEDL 76
Cdd:cd02737    11 AISEPAYKALLD--PPQSLESSPLELLKEVLECRSKSKSKENDRRVilslhlckcdhGFEyERAALEVKNHLERVTLEDL 88

                          90
                  ....*....|..
gi 1820722648  77 ASKAKVAFGQPM 88
Cdd:cd02737    89 ATTSMIKYSPQA 100
 
Name Accession Description Interval E-value
PB1_Mekk2_3 cd06405
The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 ...
 52-129 6.65e-40

The PB1 domain is present in the two mitogen-activated protein kinase kinases MEKK2 and MEKK3 which are two members of the signaling kinase cascade involved in angiogenesis and early cardiovascular development. The PB1 domain of MEKK2 (and/or MEKK3) interacts with the PB1 domain of another member of the kinase cascade Map2k5. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domains, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants. The MEKK2 and MEKK3 proteins contain a type II PB1 domain.


Pssm-ID: 99726  Cd Length: 79  Bit Score: 132.13  E-value: 6.65e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1820722648  52 VRVKFEHRGEKRILQFLRPVKLEDLASKAKVAFGQPMDLHYSNNELVIPLTTQDDLDKAVELLDRSVHMKSLKILLVI 129
Cdd:cd06405     1 VRIKFEHNGEKRIIQFPRPVKFKDLQQKVTTAFGQPMDLHYTNNELLIPLKNQEDLDRAIELLDRSPHMKSLRILLSA 78
PB1 smart00666
PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. ...
 51-128 2.18e-13

PB1 domain; Phox and Bem1p domain, present in many eukaryotic cytoplasmic signalling proteins. The domain adopts a beta-grasp fold, similar to that found in ubiquitin and Ras-binding domains. A motif, variously termed OPR, PC and AID, represents the most conserved region of the majority of PB1 domains, and is necessary for PB1 domain function. This function is the formation of PB1 domain heterodimers, although not all PB1 domain pairs associate.


Pssm-ID: 214770  Cd Length: 81  Bit Score: 63.38  E-value: 2.18e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648   51 DVRVKFEHRGEKRILQFLRPVKLEDLASKAKVAFG---QPMDLHYSNNEL-VIPLTTQDDLDKAVELLDRSvHMKSLKIL 126
Cdd:smart00666   1 TVDVKLRYGGETRRLSVPRDISFEDLRSKVAKRFGldnQSFTLKYQDEDGdLVSLTSDEDLEEAIEEYDSL-GSKKLRLH 79


                   ..
gi 1820722648  127 LV 128
Cdd:smart00666  80 VF 81
PB1 pfam00564
PB1 domain;
51-128 2.88e-12

PB1 domain;


Pssm-ID: 395447  Cd Length: 84  Bit Score: 60.77  E-value: 2.88e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648  51 DVRVKFEHRGEK-RILQFLRPVKLEDLASKAKVAFGQPM---DLHYSNNEL-VIPLTTQDDLDKAVELLDRSVhMKSLKI 125
Cdd:pfam00564   1 TVRLKLRYGGGIrRFLSVSRGISFEELRALVEQRFGLDDvdfKLKYPDEDGdLVSLTSDEDLEEALEEARSLG-SKSLRL 79


                  ...
gi 1820722648 126 LLV 128
Cdd:pfam00564  80 HVF 82
PB1 cd05992
The PB1 domain is a modular domain mediating specific protein-protein interactions which play ...
 52-127 7.31e-11

The PB1 domain is a modular domain mediating specific protein-protein interactions which play a role in many critical cell processes, such as osteoclastogenesis, angiogenesis, early cardiovascular development, and cell polarity. A canonical PB1-PB1 interaction, which involves heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. Interactions of PB1 domains with other protein domains have been described as a noncanonical PB1-interactions. The PB1 domain module is conserved in amoebas, fungi, animals, and plants.


Pssm-ID: 99716 [Multi-domain]  Cd Length: 81  Bit Score: 56.52  E-value: 7.31e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648  52 VRVKFEHRGEKRILQF-LRPVKLEDLASKAKVAFGQP---MDLHYSNNEL-VIPLTTQDDLDKAVELLDRSvHMKSLKIL 126
Cdd:cd05992     1 VRVKVKYGGEIRRFVVvSRSISFEDLRSKIAEKFGLDavsFKLKYPDEDGdLVTISSDEDLEEAIEEARRS-GSKKLRLF 79


                  .
gi 1820722648 127 L 127
Cdd:cd05992    80 V 80
RNAP_IV_NRPD1_C cd02737
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ...
 9-88 8.42e-03

Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.


Pssm-ID: 132724 [Multi-domain]  Cd Length: 381  Bit Score: 37.02  E-value: 8.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820722648   9 SIEQQALNSIMQdlAVLHKASRPALPVQETGKPKSSSPKKQNDVRV-----------KFE-HRGEKRILQFLRPVKLEDL 76
Cdd:cd02737    11 AISEPAYKALLD--PPQSLESSPLELLKEVLECRSKSKSKENDRRVilslhlckcdhGFEyERAALEVKNHLERVTLEDL 88

                          90
                  ....*....|..
gi 1820722648  77 ASKAKVAFGQPM 88
Cdd:cd02737    89 ATTSMIKYSPQA 100
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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