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Conserved domains on  [gi|1081111602|gb|OFS60953|]
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iron-sulfur cluster assembly scaffold protein NifU [Staphylococcus sp. HMSC034G11]

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 ...
 6-139 4.27e-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 TIGR01994:

Pssm-ID: 444957  Cd Length: 137  Bit Score: 174.82  E-value: 4.27e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   6 LDQLYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1081111602  86 GEAMQMSQEFTKMMLGEDYEITEE-MGDIEALQGVSQFPARIKCATLAWKALEKG 139
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETDEDEEkLGDAEALAGVAKFPARIKCATLAWKALERA 135
 
Name Accession Description Interval E-value
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 6-139 4.27e-57

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: 174.82  E-value: 4.27e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   6 LDQLYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1081111602  86 GEAMQMSQEFTKMMLGEDYEITEE-MGDIEALQGVSQFPARIKCATLAWKALEKG 139
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETDEDEEkLGDAEALAGVAKFPARIKCATLAWKALERA 135
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 5-146 3.70e-49

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


Pssm-ID: 440584  Cd Length: 128  Bit Score: 154.22  E-value: 3.70e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   5 NLDQLYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHS 84
Cdd:COG0822     1 DLDDLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDDGRIEDAKFEGFGCAISQASASMLTELVKGKT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1081111602  85 LGEAMqmsqeftkmmlgedyEITEEMGDIEALQGVSQFPARIKCATLAWKALEKGTVEKEGK 146
Cdd:COG0822    81 LEEAL---------------ALTDEFGDLAALGGLPKFPARVKCALLAWDALKAALADYRAK 127
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 9-138 5.64e-42

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: 135.84  E-value: 5.64e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   9 LYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSLGEA 88
Cdd:cd06664     1 LYSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVEDGRITDAKFQGFGCAISIASASLLTELIKGKTLDEA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1081111602  89 MQMSQEFTKMMLGEDyeiteemgDIEALQGVSQFPARIKCATLAWKALEK 138
Cdd:cd06664    81 LKLLNKDIAMLDGKE--------ELAALAGVGLPPARIHCALLAWKALKA 122
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 9-129 7.01e-32

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: 110.19  E-value: 7.01e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   9 LYRSVIMDHYKNPRNKGVL-DNGSMTVDMNNPTCGDRIRLTFDIED--GIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:pfam01592   1 LYTDKVLDHYKNPRNVGVLeDADAGVGDVGNPACGDAMRLQIKVDEstDRIEDAKFKTFGCGSAIASSSMLTELVKGKTI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1081111602  86 GEAMQMSQE--FTKMM-LGEDYEITEEMGDIEALQGVSQFPARIKCA 129
Cdd:pfam01592  81 EEALKITNTdiAEELGgLPPVKMHCSVLADDALKAAIADYPGKNKCA 127
 
Name Accession Description Interval E-value
SUF_scaf_2 TIGR01994
SUF system FeS assembly protein, NifU family; Three iron-sulfur cluster assembly systems are ...
 6-139 4.27e-57

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: 174.82  E-value: 4.27e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   6 LDQLYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:TIGR01994   1 LDSLYRQVILDHYKNPRHRGKLEDATVQERGHNPTCGDEITLTVKLEGDRIEDIAFEGEGCSISQASASMMTELIKGKTV 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1081111602  86 GEAMQMSQEFTKMMLGEDYEITEE-MGDIEALQGVSQFPARIKCATLAWKALEKG 139
Cdd:TIGR01994  81 EEALSLVEAFSEMIQGQETDEDEEkLGDAEALAGVAKFPARIKCATLAWKALERA 135
IscU COG0822
Fe-S cluster assembly scaffold protein IscU, NifU family [Posttranslational modification, ...
 5-146 3.70e-49

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


Pssm-ID: 440584  Cd Length: 128  Bit Score: 154.22  E-value: 3.70e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   5 NLDQLYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHS 84
Cdd:COG0822     1 DLDDLYSEKILDHAKNPRNVGELEDADGSGEGGNPLCGDTVTLYLKVDDGRIEDAKFEGFGCAISQASASMLTELVKGKT 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1081111602  85 LGEAMqmsqeftkmmlgedyEITEEMGDIEALQGVSQFPARIKCATLAWKALEKGTVEKEGK 146
Cdd:COG0822    81 LEEAL---------------ALTDEFGDLAALGGLPKFPARVKCALLAWDALKAALADYRAK 127
IscU_like cd06664
Iron-sulfur cluster scaffold-like proteins; IscU_like and NifU_like proteins. IscU and NifU ...
 9-138 5.64e-42

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: 135.84  E-value: 5.64e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   9 LYRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSLGEA 88
Cdd:cd06664     1 LYSEIILDHYRNPRNVGRLEDADGTGEVGNPLCGDEITLYLKVEDGRITDAKFQGFGCAISIASASLLTELIKGKTLDEA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1081111602  89 MQMSQEFTKMMLGEDyeiteemgDIEALQGVSQFPARIKCATLAWKALEK 138
Cdd:cd06664    81 LKLLNKDIAMLDGKE--------ELAALAGVGLPPARIHCALLAWKALKA 122
NifU_N pfam01592
NifU-like N terminal domain; This domain is found in NifU in combination with pfam01106. This ...
 9-129 7.01e-32

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: 110.19  E-value: 7.01e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602   9 LYRSVIMDHYKNPRNKGVL-DNGSMTVDMNNPTCGDRIRLTFDIED--GIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:pfam01592   1 LYTDKVLDHYKNPRNVGVLeDADAGVGDVGNPACGDAMRLQIKVDEstDRIEDAKFKTFGCGSAIASSSMLTELVKGKTI 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1081111602  86 GEAMQMSQE--FTKMM-LGEDYEITEEMGDIEALQGVSQFPARIKCA 129
Cdd:pfam01592  81 EEALKITNTdiAEELGgLPPVKMHCSVLADDALKAAIADYPGKNKCA 127
NifU_clost TIGR03419
FeS cluster assembly scaffold protein NifU, Clostridium type; NifU and NifS form a pair of ...
 10-138 4.17e-19

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: 77.47  E-value: 4.17e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602  10 YRSVIMDHYKNPRNKGVLDNGSMTVDMNNPTCGDRIRLTFDIEDGIINDAKFEGEGCSISMSSASMMTEAVKGHSLGEAM 89
Cdd:TIGR03419   1 YSEKVMDHFMNPRNVGEIENADGVGEVGNPKCGDIMKIFLKVEDDIIKDVKFKTFGCGAAIASSSMATEMIKGKTLEEAW 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1081111602  90 QMSQEFTkmmlgedyeiteemgdIEALQGVSqfPARIKCATLAWKALEK 138
Cdd:TIGR03419  81 ELTNKAV----------------AEALDGLP--PVKMHCSVLAEEAIHK 111
iscU TIGR01999
FeS cluster assembly scaffold IscU; This model represents IscU, a homolog of the N-terminal ...
 10-136 1.73e-17

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: 73.24  E-value: 1.73e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081111602  10 YRSVIMDHYKNPRNKGVLDNGSMTVD---MNNPTCGDRIRLTFDI-EDGIINDAKFEGEGCSISMSSASMMTEAVKGHSL 85
Cdd:TIGR01999   1 YSEKVIDHYENPRNVGSLDKDDKNVGtglVGAPACGDVMKLQIKVnDDGIIEDAKFKTFGCGSAIASSSLATELIKGKSL 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1081111602  86 GEAMQMsqeftkmmlgEDYEITEEMgdiealqgvSQFPARIKCATLAWKAL 136
Cdd:TIGR01999  81 EEALKI----------KNTEIAKEL---------SLPPVKLHCSLLAEDAI 112
TSCPD pfam12637
TSCPD domain; This family of proteins is found in bacteria, archaea and viruses. The domain is ...
 40-66 2.28e-03

TSCPD domain; This family of proteins is found in bacteria, archaea and viruses. The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulfur cluster. This domain is found at the C-terminus of some ribonucleoside-diphosphate reductase enzymes.


Pssm-ID: 463651 [Multi-domain]  Cd Length: 74  Bit Score: 34.75  E-value: 2.28e-03
                          10        20
                  ....*....|....*....|....*..
gi 1081111602  40 TCGDRIrlTFDIEDGIINDAKFEGeGC 66
Cdd:pfam12637   6 TCSREI--DFEVDDGIIKNVKFTG-GC 29
 
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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