Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA ...
3065-3408
0e+00
Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component.
The actual alignment was detected with superfamily member pfam12777:
Pssm-ID: 463699 [Multi-domain] Cd Length: 344 Bit Score: 700.29 E-value: 0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic ...
1830-2156
0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6). This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site.
:
Pssm-ID: 463697 [Multi-domain] Cd Length: 327 Bit Score: 653.01 E-value: 0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains ...
212-787
0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.
:
Pssm-ID: 462457 Cd Length: 560 Bit Score: 629.99 E-value: 0e+00
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic ...
1290-1696
3.65e-155
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (pfam08385) in many members of this family. No functions seem to have been attributed specifically to this region.
:
Pssm-ID: 462462 [Multi-domain] Cd Length: 402 Bit Score: 487.54 E-value: 3.65e-155
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. ...
3434-3652
4.18e-106
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk.
:
Pssm-ID: 463702 [Multi-domain] Cd Length: 222 Bit Score: 339.03 E-value: 4.18e-106
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of ...
3893-3913
3.20e-04
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained.
The actual alignment was detected with superfamily member pfam03028:
Pssm-ID: 460782 Cd Length: 115 Bit Score: 42.82 E-value: 3.20e-04
Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA ...
3065-3408
0e+00
Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component.
Pssm-ID: 463699 [Multi-domain] Cd Length: 344 Bit Score: 700.29 E-value: 0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic ...
1830-2156
0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6). This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site.
Pssm-ID: 463697 [Multi-domain] Cd Length: 327 Bit Score: 653.01 E-value: 0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains ...
212-787
0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.
Pssm-ID: 462457 Cd Length: 560 Bit Score: 629.99 E-value: 0e+00
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic ...
1290-1696
3.65e-155
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (pfam08385) in many members of this family. No functions seem to have been attributed specifically to this region.
Pssm-ID: 462462 [Multi-domain] Cd Length: 402 Bit Score: 487.54 E-value: 3.65e-155
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. ...
3434-3652
4.18e-106
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk.
Pssm-ID: 463702 [Multi-domain] Cd Length: 222 Bit Score: 339.03 E-value: 4.18e-106
P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA ...
2793-3052
3.67e-103
P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor.
Pssm-ID: 463701 [Multi-domain] Cd Length: 259 Bit Score: 332.27 E-value: 3.67e-103
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of ...
3893-3913
3.20e-04
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained.
Pssm-ID: 460782 Cd Length: 115 Bit Score: 42.82 E-value: 3.20e-04
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
2142-2172
9.57e-04
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350795 [Multi-domain] Cd Length: 183 Bit Score: 43.01 E-value: 9.57e-04
Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA ...
3065-3408
0e+00
Microtubule-binding stalk of dynein motor; the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component.
Pssm-ID: 463699 [Multi-domain] Cd Length: 344 Bit Score: 700.29 E-value: 0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic ...
1830-2156
0e+00
Hydrolytic ATP binding site of dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities: AAA1-AAA6). This is the first site (out of four nucleotide binding sites in the dynein motor) where the movement depends on ATP hydrolysis. When this site is nucleotide free or bound to ADP, the microtubule binding domain (MTBD) binds to the microtubule and the linker adopts the straight post-power-stroke conformation. Upon ATP binding and hydrolysis, the MTBD detaches from the microtubule and the linker is primed into the pre-power-stroke conformation. Dynein's AAA+ domains are each divided into an alpha/beta large subdomain designated with an L and and alpha small subdomains designated with an S. This is the AAA1 large (AAA1L) subdomain with the accompanying small subdomain (AAA1S). AAA1L, AAA1S and AAA2L enclose ADP.vanadate (ADP.Vi, ATP-hydrolysis transition state analogue). The AAA1L sensor-I loop, which varies in position depending on dynein's nucleotide state, swings in to contact AAA2L forming the important AAA1 nucleotide-binding site.
Pssm-ID: 463697 [Multi-domain] Cd Length: 327 Bit Score: 653.01 E-value: 0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains ...
212-787
0e+00
Dynein heavy chain, N-terminal region 1; Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit. The region featured in this family includes the sequences implicated in mediating these interactions. It is thought to be flexible and not to adopt a rigid conformation.
Pssm-ID: 462457 Cd Length: 560 Bit Score: 629.99 E-value: 0e+00
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic ...
1290-1696
3.65e-155
Dynein heavy chain, N-terminal region 2; Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. This region is found C-terminal to the dynein heavy chain N-terminal region 1 (pfam08385) in many members of this family. No functions seem to have been attributed specifically to this region.
Pssm-ID: 462462 [Multi-domain] Cd Length: 402 Bit Score: 487.54 E-value: 3.65e-155
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. ...
3434-3652
4.18e-106
ATP-binding dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk.
Pssm-ID: 463702 [Multi-domain] Cd Length: 222 Bit Score: 339.03 E-value: 4.18e-106
P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA ...
2793-3052
3.67e-103
P-loop containing dynein motor region D4; The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor.
Pssm-ID: 463701 [Multi-domain] Cd Length: 259 Bit Score: 332.27 E-value: 3.67e-103
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ...
2439-2616
1.38e-91
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs).
Pssm-ID: 463698 [Multi-domain] Cd Length: 179 Bit Score: 295.46 E-value: 1.38e-91
Dynein heavy chain AAA lid domain; This entry corresponds to the extension domain of AAA ...
2315-2430
1.15e-30
Dynein heavy chain AAA lid domain; This entry corresponds to the extension domain of AAA domain 5 in the dynein heavy chain. This domain is composed of 8 alpha helices.
Pssm-ID: 465532 [Multi-domain] Cd Length: 126 Bit Score: 118.92 E-value: 1.15e-30
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of ...
3893-3913
3.20e-04
Dynein heavy chain region D6 P-loop domain; This family represents the C-terminal region of dynein heavy chain. The chain also contains ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. Dynein is also involved in cilia and flagella movement. The dynein subunit consists of at least two heavy chains and a number of intermediate and light chains. The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This C-terminal domain carries the D6 region of the dynein motor where the P-loop has been lost in evolution but the general structure of a potential ATP binding site appears to be retained.
Pssm-ID: 460782 Cd Length: 115 Bit Score: 42.82 E-value: 3.20e-04
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like ...
2142-2172
9.57e-04
DEAD-box helicase domain of Pif1; Pif1 and other members of this family are RecD-like helicases involved in maintaining genome stability through unwinding double-stranded DNAs (dsDNAs), DNA/RNA hybrids, and G quadruplex (G4) structures. The members of Pif1 helicase subfamily studied so far all appear to contribute to telomere maintenance. Pif1 is a member of the DEAD-like helicases superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
Pssm-ID: 350795 [Multi-domain] Cd Length: 183 Bit Score: 43.01 E-value: 9.57e-04
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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