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Conserved domains on  [gi|148368987|ref|NP_055366|]
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condensin-2 complex subunit H2 isoform 1 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CNDH2_N pfam06278
Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of ...
 6-125 2.67e-74

Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII is concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII.


:

Pssm-ID: 461866  Cd Length: 117  Bit Score: 223.25  E-value: 2.67e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987    6 ARFAHLLQPIRDLTKNWEVDVAAQLGEYLEELDQICISFDEGKTTMNFIEAALLIQGSACVYSKKVEYLYSLVYQALDFI 85
Cdd:pfam06278   1 SRFAHLLQPIRDLAKNWNVDIASELEEYLLELESITITFDGGKTTLNFAEAALLIQGSACVYSRKVEYLYSLVYQTLEFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 148368987   86 SGKRRAKQLSSVQEDranGVASSGVPQEAENEFLSLDDFP 125
Cdd:pfam06278  81 SQKKKQKQNSSIESD---GNDSDAVDGEEEDEFLSLDDIP 117
CNDH2_M super family cl25166
Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the ...
 149-254 1.60e-17

Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. This region represents the disordered section of CNDH2 between the N- and the C-termini.


The actual alignment was detected with superfamily member pfam16869:

Pssm-ID: 435617  Cd Length: 126  Bit Score: 76.83  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987  149 PMALVAPD-EMEKNNNPLYSRQGEVLASRKDFRMNTCVPHPRGAFMLEPEGMSPMEPAGVSPMPGT-----------QKD 216
Cdd:pfam16869   3 PAALLPLEgDTEKDGGELDSYLGATLGSRRDFLMNTCDAHASGAFLLDLAGKSLADELLSVSSKPSsqpsksrskafSSP 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 148368987  217 TGRTEEQPMEVSVCRSPVPALGFSQEPGPSPEGPMPLG 254
Cdd:pfam16869  83 NGRSGGAGDKSEPGKNPDNNIPESDDADNDGAGDLHYD 120
 
Name Accession Description Interval E-value
CNDH2_N pfam06278
Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of ...
 6-125 2.67e-74

Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII is concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII.


Pssm-ID: 461866  Cd Length: 117  Bit Score: 223.25  E-value: 2.67e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987    6 ARFAHLLQPIRDLTKNWEVDVAAQLGEYLEELDQICISFDEGKTTMNFIEAALLIQGSACVYSKKVEYLYSLVYQALDFI 85
Cdd:pfam06278   1 SRFAHLLQPIRDLAKNWNVDIASELEEYLLELESITITFDGGKTTLNFAEAALLIQGSACVYSRKVEYLYSLVYQTLEFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 148368987   86 SGKRRAKQLSSVQEDranGVASSGVPQEAENEFLSLDDFP 125
Cdd:pfam06278  81 SQKKKQKQNSSIESD---GNDSDAVDGEEEDEFLSLDDIP 117
CNDH2_M pfam16869
Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the ...
 149-254 1.60e-17

Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. This region represents the disordered section of CNDH2 between the N- and the C-termini.


Pssm-ID: 435617  Cd Length: 126  Bit Score: 76.83  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987  149 PMALVAPD-EMEKNNNPLYSRQGEVLASRKDFRMNTCVPHPRGAFMLEPEGMSPMEPAGVSPMPGT-----------QKD 216
Cdd:pfam16869   3 PAALLPLEgDTEKDGGELDSYLGATLGSRRDFLMNTCDAHASGAFLLDLAGKSLADELLSVSSKPSsqpsksrskafSSP 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 148368987  217 TGRTEEQPMEVSVCRSPVPALGFSQEPGPSPEGPMPLG 254
Cdd:pfam16869  83 NGRSGGAGDKSEPGKNPDNNIPESDDADNDGAGDLHYD 120
 
Name Accession Description Interval E-value
CNDH2_N pfam06278
Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of ...
 6-125 2.67e-74

Condensin II complex subunit CAP-H2 or CNDH2, N-terminal; CNDH2_N is the N-terminal domain of the H2 subunit of the condensing II complex, found in eukaryotes but not in fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII is concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII.


Pssm-ID: 461866  Cd Length: 117  Bit Score: 223.25  E-value: 2.67e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987    6 ARFAHLLQPIRDLTKNWEVDVAAQLGEYLEELDQICISFDEGKTTMNFIEAALLIQGSACVYSKKVEYLYSLVYQALDFI 85
Cdd:pfam06278   1 SRFAHLLQPIRDLAKNWNVDIASELEEYLLELESITITFDGGKTTLNFAEAALLIQGSACVYSRKVEYLYSLVYQTLEFL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 148368987   86 SGKRRAKQLSSVQEDranGVASSGVPQEAENEFLSLDDFP 125
Cdd:pfam06278  81 SQKKKQKQNSSIESD---GNDSDAVDGEEEDEFLSLDDIP 117
CNDH2_M pfam16869
Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the ...
 149-254 1.60e-17

Condensin II complex subunit CAP-H2 or CNDH2, mid domain; CNDH2_M is the middle domain of the H2 subunit of the condensin II complex, found in eukaryotes but not fungi. Eukaryotes carry at least two condensin complexes, I and II, each made up of five subunits. The functions of the two complexes are collaborative but non-overlapping. CI appears to be functional in G2 phase in the cytoplasm beginning the process of chromosomal lateral compaction while the CII are concentrated in the nucleus, possibly to counteract the activity of cohesion at this stage. In prophase, CII contributes to axial shortening of chromatids while CI continues to bring about lateral chromatid compaction, during which time the sister chromatids are joined centrally by cohesins. There appears to be just one condensin complex in fungi. CI and CII each contain SMC2 and SMC4 (structural maintenance of chromosomes) subunits, then CI has non-SMC CAP-D2 (CND1), CAP-G (CND3), and CAP-H (CND2). CII has, in addition to the two SMCs, CAP-D3, CAPG2 and CAP-H2. All four of the CAP-D and CAP-G subunits have degenerate HEAT repeats, whereas the CAP-H are kleisins or SMC-interacting proteins (ie they bind directly to the SMC subunits in the complex). The SMC molecules are each long with a small hinge-like knob at the free end of a longish strand, articulating with each other at the hinge. Each strand ends in a knob-like head that binds to one or other end of the CAP-H subunit. The HEAT-repeat containing D and G subunits bind side-by-side between the ends of the H subunit. Activity of the various parts of the complex seem to be triggered by extensive phosphorylations, eg, entry of the complex, in Sch.pombe, into the nucleus during mitosis is promoted by Cdk1 phosphorylation of SMC4/Cut3; and it has been shown that Cdk1 phosphorylates CAP-D3 at Thr1415 in He-La cells thus promoting early stage chromosomal condensation by CII. This region represents the disordered section of CNDH2 between the N- and the C-termini.


Pssm-ID: 435617  Cd Length: 126  Bit Score: 76.83  E-value: 1.60e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 148368987  149 PMALVAPD-EMEKNNNPLYSRQGEVLASRKDFRMNTCVPHPRGAFMLEPEGMSPMEPAGVSPMPGT-----------QKD 216
Cdd:pfam16869   3 PAALLPLEgDTEKDGGELDSYLGATLGSRRDFLMNTCDAHASGAFLLDLAGKSLADELLSVSSKPSsqpsksrskafSSP 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 148368987  217 TGRTEEQPMEVSVCRSPVPALGFSQEPGPSPEGPMPLG 254
Cdd:pfam16869  83 NGRSGGAGDKSEPGKNPDNNIPESDDADNDGAGDLHYD 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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