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Conserved domains on  [gi|2258880622|gb|USO00939|]
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MAG: iron-sulfur cluster assembly scaffold protein [Alphaproteobacteria bacterium]

Protein Classification

iron-sulfur cluster assembly scaffold protein( domain architecture ID 880)

iron-sulfur cluster assembly scaffold protein, similar to Thermotoga maritima IscU, on which IscS assembles Fe-S clusters

CATH:  3.90.1010.10
Gene Ontology:  GO:0016226|GO:0051536
PubMed:  15952888|15379587
SCOP:  4001402

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IscU_like super family cl00528
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 2-117 9.18e-57

Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.


The actual alignment was detected with superfamily member TIGR01999:

Pssm-ID: 444957  Cd Length: 124  Bit Score: 172.24  E-value: 9.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDPNVGVGFVGSPACGDVLKIFIKVDDEDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:TIGR01999   9 YENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2258880622  82 KEIADELALPPIKTHCSVLAEEAILDAIYDLLKKRK 117
Cdd:TIGR01999  89 TEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQE 124
 
Name Accession Description Interval E-value
iscU TIGR01999
FeS cluster assembly scaffold IscU; This model represents IscU, a homolog of the N-terminal ...
 2-117 9.18e-57

FeS cluster assembly scaffold IscU; This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 188192  Cd Length: 124  Bit Score: 172.24  E-value: 9.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDPNVGVGFVGSPACGDVLKIFIKVDDEDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:TIGR01999   9 YENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2258880622  82 KEIADELALPPIKTHCSVLAEEAILDAIYDLLKKRK 117
Cdd:TIGR01999  89 TEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQE 124
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 2-117 2.40e-50

NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.


Pssm-ID: 426336  Cd Length: 127  Bit Score: 156.03  E-value: 2.40e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDPnvGVGFVGSPACGDVLKIFIKVDDE-DRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKIT 80
Cdd:pfam01592  10 YKNPRNVGVLEDADA--GVGDVGNPACGDAMRLQIKVDEStDRIEDAKFKTFGCGSAIASSSMLTELVKGKTIEEALKIT 87

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2258880622  81 NKEIADEL-ALPPIKTHCSVLAEEAILDAIYDLLKKRK 117
Cdd:pfam01592  88 NTDIAEELgGLPPVKMHCSVLADDALKAAIADYPGKNK 125
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 2-116 1.84e-40

Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440584  Cd Length: 128  Bit Score: 131.11  E-value: 1.84e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:COG0822    14 AKNPRNVGELEDAD---GSGEGGNPLCGDTVTLYLKVDD-GRIEDAKFEGFGCAISQASASMLTELVKGKTLEEALALTD 89

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2258880622  82 K--EIADELALP--PIKTHCSVLAEEAILDAIYDLLKKR 116
Cdd:COG0822    90 EfgDLAALGGLPkfPARVKCALLAWDALKAALADYRAKK 128
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 2-108 7.36e-39

Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.


Pssm-ID: 143480  Cd Length: 123  Bit Score: 126.60  E-value: 7.36e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:cd06664    10 YRNPRNVGRLEDAD---GTGEVGNPLCGDEITLYLKVED-GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2258880622  82 KEIADE-----------LALPPIKTHCSVLAEEAILDA 108
Cdd:cd06664    86 KDIAMLdgkeelaalagVGLPPARIHCALLAWKALKAA 123
 
Name Accession Description Interval E-value
iscU TIGR01999
FeS cluster assembly scaffold IscU; This model represents IscU, a homolog of the N-terminal ...
 2-117 9.18e-57

FeS cluster assembly scaffold IscU; This model represents IscU, a homolog of the N-terminal region of NifU, an Fe-S cluster assembly protein found mostly in nitrogen-fixing bacteria. IscU is considered part of the IscSUA-hscAB-fdx system of Fe-S assembly, whereas NifU is found in nitrogenase-containing (nitrogen-fixing) species. A NifU-type protein is also found in Helicobacter and Campylobacter. IscU and NifU are considered scaffold proteins on which Fe-S clusters are assembled before transfer to apoproteins. This model excludes true NifU proteins as in Klebsiella pneumoniae and Anabaena sp. as well as archaeal homologs. It includes largely proteobacterial and eukaryotic forms. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 188192  Cd Length: 124  Bit Score: 172.24  E-value: 9.18e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDPNVGVGFVGSPACGDVLKIFIKVDDEDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:TIGR01999   9 YENPRNVGSLDKDDKNVGTGLVGAPACGDVMKLQIKVNDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSLEEALKIKN 88

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2258880622  82 KEIADELALPPIKTHCSVLAEEAILDAIYDLLKKRK 117
Cdd:TIGR01999  89 TEIAKELSLPPVKLHCSLLAEDAIKAAIKDYKSKQE 124
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 2-117 2.40e-50

NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.


Pssm-ID: 426336  Cd Length: 127  Bit Score: 156.03  E-value: 2.40e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDPnvGVGFVGSPACGDVLKIFIKVDDE-DRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKIT 80
Cdd:pfam01592  10 YKNPRNVGVLEDADA--GVGDVGNPACGDAMRLQIKVDEStDRIEDAKFKTFGCGSAIASSSMLTELVKGKTIEEALKIT 87

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2258880622  81 NKEIADEL-ALPPIKTHCSVLAEEAILDAIYDLLKKRK 117
Cdd:pfam01592  88 NTDIAEELgGLPPVKMHCSVLADDALKAAIADYPGKNK 125
NifU_clost TIGR03419
FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of ...
 2-116 2.81e-46

FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 132460  Cd Length: 121  Bit Score: 145.65  E-value: 2.81e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:TIGR03419   9 FMNPRNVGEIENAD---GVGEVGNPKCGDIMKIFLKVED-DIIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTN 84

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2258880622  82 KEIADEL-ALPPIKTHCSVLAEEAILDAIYDLLKKR 116
Cdd:TIGR03419  85 KAVAEALdGLPPVKMHCSVLAEEAIHKAINDYREKN 120
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 2-116 1.84e-40

Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440584  Cd Length: 128  Bit Score: 131.11  E-value: 1.84e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:COG0822    14 AKNPRNVGELEDAD---GSGEGGNPLCGDTVTLYLKVDD-GRIEDAKFEGFGCAISQASASMLTELVKGKTLEEALALTD 89

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2258880622  82 K--EIADELALP--PIKTHCSVLAEEAILDAIYDLLKKR 116
Cdd:COG0822    90 EfgDLAALGGLPkfPARVKCALLAWDALKAALADYRAKK 128
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 2-108 7.36e-39

Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU function as a scaffold for the assembly of [2Fe-2S] clusters before they are transferred to apo target proteins. They are highly conserved and play vital roles in the ISC and NIF systems of Fe-S protein maturation. NIF genes participate in nitrogen fixation in several isolated bacterial species. The NifU domain, however, is also found in bacteria that do not fix nitrogen, so it may have wider significance in the cell. Human IscU interacts with frataxin, the Friedreich ataxia gene product, and incorrectly spliced IscU has been shown to disrupt iron homeostasis in skeletal muscle and cause myopathy.


Pssm-ID: 143480  Cd Length: 123  Bit Score: 126.60  E-value: 7.36e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKITN 81
Cdd:cd06664    10 YRNPRNVGRLEDAD---GTGEVGNPLCGDEITLYLKVED-GRITDAKFQGFGCAISIASASLLTELIKGKTLDEALKLLN 85

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 2258880622  82 KEIADE-----------LALPPIKTHCSVLAEEAILDA 108
Cdd:cd06664    86 KDIAMLdgkeelaalagVGLPPARIHCALLAWKALKAA 123
NifU_proper TIGR02000
Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster ...
 2-111 1.53e-37

Fe-S cluster assembly protein NifU; Three different but partially homologous Fe-S cluster assembly systems have been described: Isc, Suf, and Nif. The latter is associated with donation of an Fe-S cluster to nitrogenase in a number of nitrogen-fixing species. NifU, described here, consists of an N-terminal domain (pfam01592) and a C-terminal domain (pfam01106). Homologs with an equivalent domain archictecture from Helicobacter and Campylobacter, however, are excluded from this model by a high trusted cutoff. The model, therefore, is specific for NifU involved in nitrogenase maturation. The related model TIGR01999 homologous to the N-terminus of this model describes IscU from the Isc system as in E. coli, Saccharomyces cerevisiae, and Homo sapiens. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other, Central intermediary metabolism, Nitrogen fixation]


Pssm-ID: 273921 [Multi-domain]  Cd Length: 290  Bit Score: 128.45  E-value: 1.53e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2258880622   2 FENPVNVGSLDENDpnvGVGFVGSPACGDVLKIFIKVD-DEDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKIT 80
Cdd:TIGR02000  12 FYNPKNAGVVEDAN---AVGEVGSISCGDALRLMLKVDpESDKIVDAGFQTFGCGSAIASSSALTEMIKGLTLDEALKVS 88

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2258880622  81 NKEIADEL-ALPPIKTHCSVLAEEAILDAIYD 111
Cdd:TIGR02000  89 NQDIADYLgGLPPEKMHCSVMGQEALEAAIAN 120
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 26-79 6.85e-10

SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are known so far. ISC is broadly distributed while NIF tends to be associated with nitrogenase in nitrogen-fixing bacteria. The most recently described is SUF, believed to be important to maintain the function during aerobic stress of enzymes with labile Fe-S clusters. It is fairly widely distributed. This family represents one of two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]


Pssm-ID: 273918  Cd Length: 137  Bit Score: 53.10  E-value: 6.85e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2258880622  26 PACGDVLKIFIKVDDeDRIVDVKFKTFGCGSAIASSAVLTQKVMGLTLDEAKKI 79
Cdd:TIGR01994  34 PTCGDEITLTVKLEG-DRIEDIAFEGEGCSISQASASMMTELIKGKTVEEALSL 86
 
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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