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Conserved domains on  [gi|578832002|ref|XP_006722341|]
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nuclear prelamin A recognition factor isoform X1 [Homo sapiens]

Protein Classification

Fe_hyd_lg_C and Fe_hyd_SSU domain-containing protein; iron hydrogenase small subunit( domain architecture ID 13562369)

Fe_hyd_lg_C and Fe_hyd_SSU domain-containing protein; iron hydrogenase small subunit is part of the iron-sulfur enzyme that catalyzes the oxidation of molecular hydrogen and is essential for hydrogen cycling

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Fe_hyd_lg_C super family cl37679
Iron only hydrogenase large subunit, C-terminal domain;
92-336 4.63e-52

Iron only hydrogenase large subunit, C-terminal domain;


The actual alignment was detected with superfamily member pfam02906:

Pssm-ID: 397172  Cd Length: 277  Bit Score: 175.50  E-value: 4.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002   92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLG-----------------------------------------W 130
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGfdyvfdtafgadltimeeateflerlekgkklpmftsccpgW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  131 VRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGADCVLT 210
Cdd:pfam02906  81 VKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAVLT 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  211 SGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDF 283
Cdd:pfam02906 151 TRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGI 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578832002  284 QEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 336
Cdd:pfam02906 225 KEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 353-401 1.16e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


:

Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.16e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578832002   353 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 401
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-336 4.63e-52

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 175.50  E-value: 4.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002   92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLG-----------------------------------------W 130
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGfdyvfdtafgadltimeeateflerlekgkklpmftsccpgW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  131 VRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGADCVLT 210
Cdd:pfam02906  81 VKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAVLT 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  211 SGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDF 283
Cdd:pfam02906 151 TRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGI 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578832002  284 QEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 336
Cdd:pfam02906 225 KEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
129-398 1.44e-36

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 138.62  E-value: 1.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 129 GWVRYAERVlgRP-ITAHLCTAKSPQQVMGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDC 207
Cdd:COG4624  225 AWVKLIEKY--YPeLLPNLSPCKSPMQAFGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DY 289

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 208 VLTSGEIAQIMEQGDLSvrdaavdtlFGDLKEDKVtrhDGASSdgHLAHIF----------RHAAKELFNEDVEevtyra 277
Cdd:COG4624  290 VLTFRELARMIKEAGID---------LANLEEEEF---DNESS--GAGRIFgvtggvmeaaLRTAYELLPDGLE------ 349

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 278 lrnkdfqevtlekngevvLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQaqtPDGHADKALLRQMEG 357
Cdd:COG4624  350 ------------------LKVAVVSGLKNCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ---PIPPGSLEKRRKRVA 408

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 578832002 358 IYADI-PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQ 398
Cdd:COG4624  409 LYAKEaPIRKSHENPEILDLYREFLGKPLSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 353-401 1.16e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.16e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578832002   353 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 401
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 348-399 9.80e-12

Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.


Pssm-ID: 460511 [Multi-domain]  Cd Length: 56  Bit Score: 59.82  E-value: 9.80e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578832002  348 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 399
Cdd:pfam02256   1 DDIRKKRAEALYKIdknKPLRKSHENPAVKKLYEEFLGEPLSHKAHELLHTHYTP 55
 
Name Accession Description Interval E-value
Fe_hyd_lg_C pfam02906
Iron only hydrogenase large subunit, C-terminal domain;
92-336 4.63e-52

Iron only hydrogenase large subunit, C-terminal domain;


Pssm-ID: 397172  Cd Length: 277  Bit Score: 175.50  E-value: 4.63e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002   92 KVLVVSVCPQSLPYFAAKFNLSVTDASRRLCGFLKSLG-----------------------------------------W 130
Cdd:pfam02906   1 KKVVAQIAPAVRGAFGEEFGLPPTVTTGKLVAALRKLGfdyvfdtafgadltimeeateflerlekgkklpmftsccpgW 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  131 VRYAERVLGRpITAHLCTAKSPQQVMGSLVKDYFARQqnlspEKIFHVIVAPCYDKKLEALQESLppalHGSRGADCVLT 210
Cdd:pfam02906  81 VKYVEKYYPE-LLPNLSTCKSPMQMFGALIKTYYAED-----LKIYVVSIMPCTAKKFEAARPEM----KGDRDVDAVLT 150

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002  211 SGEIAQIMEQGDL---SVRDAAVDTLFGDlkedkvTRHDG---ASSDGHLAHIFRHAAKELFNEDVEEVTYRALRN-KDF 283
Cdd:pfam02906 151 TRELAAMIKEAGIdfaKLEDEEFDNPLGE------SSGAGrifGVTGGVMEAALRTAYELLTGKELPAIEFKEVRGlEGI 224

                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 578832002  284 QEVTLEKNGeVVLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNG 336
Cdd:pfam02906 225 KEATVEIGG-TTVKVAVVSGLKNARKLLEKIKAGELKYHFIEVMACPGGCIGG 276
Nar1 COG4624
Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];
129-398 1.44e-36

Iron only hydrogenase large subunit, C-terminal domain [Energy production and conversion];


Pssm-ID: 443663 [Multi-domain]  Cd Length: 450  Bit Score: 138.62  E-value: 1.44e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 129 GWVRYAERVlgRP-ITAHLCTAKSPQQVMGSLVKDYFArqqnlspEKIFHVIVAPCYDKKLEALQESLPPALhgsrgaDC 207
Cdd:COG4624  225 AWVKLIEKY--YPeLLPNLSPCKSPMQAFGALIKTYYA-------PDIKVVFIGPCIAKKFEAKRPEMKGDV------DY 289

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 208 VLTSGEIAQIMEQGDLSvrdaavdtlFGDLKEDKVtrhDGASSdgHLAHIF----------RHAAKELFNEDVEevtyra 277
Cdd:COG4624  290 VLTFRELARMIKEAGID---------LANLEEEEF---DNESS--GAGRIFgvtggvmeaaLRTAYELLPDGLE------ 349

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832002 278 lrnkdfqevtlekngevvLRFAAAYGFRNIQNMILKLKKGKFPFHFVEVLACAGGCLNGRGQaqtPDGHADKALLRQMEG 357
Cdd:COG4624  350 ------------------LKVAVVSGLKNCRKLLEEIKAGKIDYHFIEVMACPGGCIGGPGQ---PIPPGSLEKRRKRVA 408

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 578832002 358 IYADI-PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQ 398
Cdd:COG4624  409 LYAKEaPIRKSHENPEILDLYREFLGKPLSEKAHELLHTHYR 450
Fe_hyd_SSU smart00902
Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, ...
 353-401 1.16e-15

Iron hydrogenase small subunit; Many microorganisms, such as methanogenic, acetogenic, nitrogen-fixing, photosynthetic, or sulphate-reducing bacteria, metabolise hydrogen. Hydrogen activation is mediated by a family of enzymes, termed hydrogenases, which either provide these organisms with reducing power from hydrogen oxidation, or act as electron sinks. There are two hydrogenases families that differ functionally from each other: NiFe hydrogenases tend to be more involved in hydrogen oxidation, while Iron-only FeFe (Fe only) hydrogenases in hydrogen production. Fe only hydrogenases show a common core structure, which contains a moiety, deeply buried inside the protein, with an Fe-Fe dinuclear centre, nonproteic bridging, terminal CO and CN- ligands attached to each of the iron atoms, and a dithio moiety, which also bridges the two iron atoms and has been tentatively assigned as a di(thiomethyl)amine. This common core also harbours three [4Fe-4S] iron-sulphur clusters. In FeFe hydrogenases, as in NiFe hydrogenases, the set of iron-sulphur clusters is dispersed regularly between the dinuclear Fe-Fe centre and the molecular surface. These clusters are distant by about 1.2 nm from each other but the [4Fe-4S] cluster closest to the dinuclear centre is covalently bound to one of the iron atoms though a thiolate bridging ligand. The moiety including the dinuclear centre, the thiolate bridging ligand, and the proximal [4Fe-4S] cluster is known as the H-cluster. A channel, lined with hydrophobic amino acid side chains, nearly connects the dinuclear centre and the molecular surface. Furthermore hydrogen-bonded water molecule sites have been identified at the interior and at the surface of the protein. The small subunit is comprised of alternating random coil and alpha helical structures that encompass the large subunit in a novel protein fold.


Pssm-ID: 214899 [Multi-domain]  Cd Length: 52  Bit Score: 70.74  E-value: 1.16e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 578832002   353 RQMEGIYADI---PVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQSQE 401
Cdd:smart00902   1 QRAEALYNIDkslPLRKSHENPAVKKLYEEFLGGPLSHKAHELLHTHYHDRE 52
Fe_hyd_SSU pfam02256
Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only ...
 348-399 9.80e-12

Iron hydrogenase small subunit; This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold.


Pssm-ID: 460511 [Multi-domain]  Cd Length: 56  Bit Score: 59.82  E-value: 9.80e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 578832002  348 DKALLRQMEGIYAD---IPVRRPESSAHVQELYQEWLEGINSPKAREVLHTTYQS 399
Cdd:pfam02256   1 DDIRKKRAEALYKIdknKPLRKSHENPAVKKLYEEFLGEPLSHKAHELLHTHYTP 55
 
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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