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Conserved domains on  [gi|6322827|ref|NP_012900|]
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Pan3p [Saccharomyces cerevisiae S288C]

Protein Classification

PAN2-PAN3 deadenylation complex subunit PAN3( domain architecture ID 15472959)

PAN2-PAN3 deadenylation complex subunit PAN3 is a regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover; PAN specifically shortens poly(A) tails of RNA and the activity is stimulated by poly(A)-binding protein PAB1; contains a catalytically inactive pseudokinase domain

CATH:  1.10.510.10
Gene Symbol:  PAN3
Gene Ontology:  GO:0008143|GO:0005524|GO:0031251|GO:0046872|GO:0006397
PubMed:  16244704|24880344|23932717

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pan3_PK pfam18101
Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A) ...
 540-675 8.50e-74

Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo. Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteriztics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases.


:

Pssm-ID: 465649  Cd Length: 138  Bit Score: 233.92  E-value: 8.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827    540 IHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQ 619
Cdd:pfam18101   1 IDELLPMIGARLLTELDAALHYNDELESELSRELENGRLFRLLCKLGFINERPEFEGDPRWSETGDRYMLKLFRDYVFHQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322827    620 VDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKELKDLIESTFR 675
Cdd:pfam18101  81 VDEQGRPVLDLGHVLSCLNKLDAGVDEKIMLTSRDEQSCLVVSYKELKKCIESAFG 136
PKc_like super family cl21453
Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the ...
 311-419 5.04e-03

Protein Kinases, catalytic domain; The protein kinase superfamily is mainly composed of the catalytic domains of serine/threonine-specific and tyrosine-specific protein kinases. It also includes RIO kinases, which are atypical serine protein kinases, aminoglycoside phosphotransferases, and choline kinases. These proteins catalyze the transfer of the gamma-phosphoryl group from ATP to hydroxyl groups in specific substrates such as serine, threonine, or tyrosine residues of proteins.


The actual alignment was detected with superfamily member cd08529:

Pssm-ID: 473864 [Multi-domain]  Cd Length: 256  Bit Score: 39.32  E-value: 5.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827  311 FKVFSNYDGKAYVLKR--LPNIDKSMNPNKISKIyQIWSKINCTNLIKFRDIFQTtkfgDLSICLVFDYYPNSlSLYDYh 388
Cdd:cd08529  17 YKVVRKVDGRVYALKQidISRMSRKMREEAIDEA-RVLSKLNSPYVIKYYDSFVD----KGKLNIVMEYAENG-DLHSL- 89

                        90       100       110
                ....*....|....*....|....*....|.
gi 6322827  389 FVNFPKFPITNNYLWIYLVQLTNVINSIHSQ 419
Cdd:cd08529  90 IKSQRGRPLPEDQIWKFFIQTLLGLSHLHSK 120
 
Name Accession Description Interval E-value
Pan3_PK pfam18101
Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A) ...
 540-675 8.50e-74

Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo. Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteriztics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases.


Pssm-ID: 465649  Cd Length: 138  Bit Score: 233.92  E-value: 8.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827    540 IHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQ 619
Cdd:pfam18101   1 IDELLPMIGARLLTELDAALHYNDELESELSRELENGRLFRLLCKLGFINERPEFEGDPRWSETGDRYMLKLFRDYVFHQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322827    620 VDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKELKDLIESTFR 675
Cdd:pfam18101  81 VDEQGRPVLDLGHVLSCLNKLDAGVDEKIMLTSRDEQSCLVVSYKELKKCIESAFG 136
STKc_FA2-like cd08529
Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii FA2 and similar ...
 311-419 5.04e-03

Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii FA2 and similar proteins; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chlamydomonas reinhardtii FA2 was discovered in a genetic screen for deflagellation-defective mutants. It is essential for basal-body/centriole-associated microtubule severing, and plays a role in cell cycle progression. No cellular function has yet been ascribed to CNK4. The Chlamydomonas reinhardtii FA2-like subfamily belongs to the (NIMA)-related kinase (Nek) family, which includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily contains FA2 and CNK4. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.


Pssm-ID: 270868 [Multi-domain]  Cd Length: 256  Bit Score: 39.32  E-value: 5.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827  311 FKVFSNYDGKAYVLKR--LPNIDKSMNPNKISKIyQIWSKINCTNLIKFRDIFQTtkfgDLSICLVFDYYPNSlSLYDYh 388
Cdd:cd08529  17 YKVVRKVDGRVYALKQidISRMSRKMREEAIDEA-RVLSKLNSPYVIKYYDSFVD----KGKLNIVMEYAENG-DLHSL- 89

                        90       100       110
                ....*....|....*....|....*....|.
gi 6322827  389 FVNFPKFPITNNYLWIYLVQLTNVINSIHSQ 419
Cdd:cd08529  90 IKSQRGRPLPEDQIWKFFIQTLLGLSHLHSK 120
 
Name Accession Description Interval E-value
Pan3_PK pfam18101
Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A) ...
 540-675 8.50e-74

Pan3 Pseudokinase domain; This is a pseudokinase (PK) domain found in PAB-dependent poly(A)-specific ribonuclease subunit pan3. PAN3 proteins contain three prominent regions: an unstructured N-terminal region (N-term), a central PK domain, and a highly conserved C-terminal domain (C-term). The PAN3 PK domain has retained its ATP binding capacity, and this function is required for mRNA degradation in vivo. Analysis of Pan3 amino acids sequences show that, despite of retaining the general structural characteriztics of protein kinases, the PK domain has substitutions in all the conserved motifs that are critical for kinase activity, such as in the catalytic VAIK and HRD motifs and in the Mg2+ binding DFG motif. However, the PAN3 PK domain has been shown to bind ATP. Furthermore, similar to other kinases, the ATP-binding site is located in the cleft between the N- and C-lobes of the kinase fold, however, the ATP-binding pocket is wider than that of typical kinases.


Pssm-ID: 465649  Cd Length: 138  Bit Score: 233.92  E-value: 8.50e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827    540 IHDLTSHFYDKMFMVLESSQTYTEYMESVLSRELENGRLFRLVNKLNCIFGRIESRIDINWSESGTKFPIILFYDYVFHQ 619
Cdd:pfam18101   1 IDELLPMIGARLLTELDAALHYNDELESELSRELENGRLFRLLCKLGFINERPEFEGDPRWSETGDRYMLKLFRDYVFHQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 6322827    620 VDSNGKPIMDLTHVLRCLNKLDAGIQEKLMLVTPDELNCIIISYKELKDLIESTFR 675
Cdd:pfam18101  81 VDEQGRPVLDLGHVLSCLNKLDAGVDEKIMLTSRDEQSCLVVSYKELKKCIESAFG 136
STKc_FA2-like cd08529
Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii FA2 and similar ...
 311-419 5.04e-03

Catalytic domain of the Serine/Threonine Kinases, Chlamydomonas reinhardtii FA2 and similar proteins; STKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine residues on protein substrates. Chlamydomonas reinhardtii FA2 was discovered in a genetic screen for deflagellation-defective mutants. It is essential for basal-body/centriole-associated microtubule severing, and plays a role in cell cycle progression. No cellular function has yet been ascribed to CNK4. The Chlamydomonas reinhardtii FA2-like subfamily belongs to the (NIMA)-related kinase (Nek) family, which includes seven different Chlamydomonas Neks (CNKs 1-6 and Fa2). This subfamily contains FA2 and CNK4. The Nek family is part of a larger superfamily that includes the catalytic domains of other STKs, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.


Pssm-ID: 270868 [Multi-domain]  Cd Length: 256  Bit Score: 39.32  E-value: 5.04e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6322827  311 FKVFSNYDGKAYVLKR--LPNIDKSMNPNKISKIyQIWSKINCTNLIKFRDIFQTtkfgDLSICLVFDYYPNSlSLYDYh 388
Cdd:cd08529  17 YKVVRKVDGRVYALKQidISRMSRKMREEAIDEA-RVLSKLNSPYVIKYYDSFVD----KGKLNIVMEYAENG-DLHSL- 89

                        90       100       110
                ....*....|....*....|....*....|.
gi 6322827  389 FVNFPKFPITNNYLWIYLVQLTNVINSIHSQ 419
Cdd:cd08529  90 IKSQRGRPLPEDQIWKFFIQTLLGLSHLHSK 120
 
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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