NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2570276357|ref|WP_307403861|]
View 

NifB/NifX family molybdenum-iron cluster-binding protein [Desulfofundulus luciae]

Protein Classification

NifB/NifX family molybdenum-iron cluster-binding protein( domain architecture ID 10003667)

NifB/NifX family molybdenum-iron cluster-binding protein may serve as a transient reservoir of FeMo-co (the iron-molybdenum cofactor of nitrogenase) precursors and help control their flux during FeMo-co synthesis

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NifX COG1433
Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein ...
 6-85 1.38e-12

Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 441042  Cd Length: 108  Bit Score: 58.74  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570276357   6 LMVDISRGGLISRRQVRLDDL----GWPSRVEQMVHLGVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYLQD 81
Cdd:COG1433    24 LIYDVEDGEIVLVEVIENPGEagggAGGLLAQLLAELGVDVVIAGGIGPGALEALEAAGIKVYTGAEGTVEEALEAYLEG 103


                  ....
gi 2570276357  82 QLNQ 85
Cdd:COG1433   104 ELEE 107
 
Name Accession Description Interval E-value
NifX COG1433
Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein ...
 6-85 1.38e-12

Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441042  Cd Length: 108  Bit Score: 58.74  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570276357   6 LMVDISRGGLISRRQVRLDDL----GWPSRVEQMVHLGVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYLQD 81
Cdd:COG1433    24 LIYDVEDGEIVLVEVIENPGEagggAGGLLAQLLAELGVDVVIAGGIGPGALEALEAAGIKVYTGAEGTVEEALEAYLEG 103


                  ....
gi 2570276357  82 QLNQ 85
Cdd:COG1433   104 ELEE 107
Nitro_FeMo-Co pfam02579
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins ...
 8-79 1.88e-06

Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.


Pssm-ID: 460602  Cd Length: 93  Bit Score: 42.25  E-value: 1.88e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2570276357   8 VDISRGG--LISRRQVRLDDLGW-PSRVEQMVHL-GVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYL 79
Cdd:pfam02579  18 YDVEEGGveVVENREPACAAGGGgGGKLAQLLADeGVDAVIVGGIGPNAAARLKAAGIKVYKGAGGTVEEALEAYL 93
MTH1175 cd00851
This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding ...
 32-79 4.35e-06

This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).


Pssm-ID: 238431  Cd Length: 103  Bit Score: 41.49  E-value: 4.35e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2570276357  32 VEQMVHLGVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYL 79
Cdd:cd00851    56 AEFLADEGVDVVIVGGIGPRALNKLRNAGIKVYKGAEGTVEEAIEALL 103
 
Name Accession Description Interval E-value
NifX COG1433
Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein ...
 6-85 1.38e-12

Predicted Fe-Mo cluster-binding protein, NifX family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 441042  Cd Length: 108  Bit Score: 58.74  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2570276357   6 LMVDISRGGLISRRQVRLDDL----GWPSRVEQMVHLGVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYLQD 81
Cdd:COG1433    24 LIYDVEDGEIVLVEVIENPGEagggAGGLLAQLLAELGVDVVIAGGIGPGALEALEAAGIKVYTGAEGTVEEALEAYLEG 103


                  ....
gi 2570276357  82 QLNQ 85
Cdd:COG1433   104 ELEE 107
Nitro_FeMo-Co pfam02579
Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins ...
 8-79 1.88e-06

Dinitrogenase iron-molybdenum cofactor; This family contains several NIF (B, Y and X) proteins which are iron-molybdenum cofactors (FeMo-co) in the dinitrogenase enzyme which catalyzes the reduction of dinitrogen to ammonium. Dinitrogenase is a hetero-tetrameric (alpha(2)beta(2)) enzyme which contains the iron-molybdenum cofactor (FeMo-co) at its active site.


Pssm-ID: 460602  Cd Length: 93  Bit Score: 42.25  E-value: 1.88e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2570276357   8 VDISRGG--LISRRQVRLDDLGW-PSRVEQMVHL-GVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYL 79
Cdd:pfam02579  18 YDVEEGGveVVENREPACAAGGGgGGKLAQLLADeGVDAVIVGGIGPNAAARLKAAGIKVYKGAGGTVEEALEAYL 93
MTH1175 cd00851
This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding ...
 32-79 4.35e-06

This uncharacterized conserved protein belongs to a family of iron-molybdenum cluster-binding proteins that includes NifX, NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).


Pssm-ID: 238431  Cd Length: 103  Bit Score: 41.49  E-value: 4.35e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2570276357  32 VEQMVHLGVEVLICGGISNFLYHQLVARGIQVIPWVTGDVEEVLQAYL 79
Cdd:cd00851    56 AEFLADEGVDVVIVGGIGPRALNKLRNAGIKVYKGAEGTVEEAIEALL 103
NifX_NifB cd00562
This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, ...
 36-79 3.89e-03

This CD represents a family of iron-molybdenum cluster-binding proteins that includes NifB, NifX, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. This domain is a predicted small-molecule-binding domain (SMBD) with an alpha/beta fold that is present either as a stand-alone domain (e.g. NifX and NifY) or fused to another conserved domain (e.g. NifB) however, its function is still undetermined.The SCOP database suggests that this domain is most similar to structures within the ribonuclease H superfamily. This conserved domain is represented in two of the three major divisions of life (bacteria and archaea).


Pssm-ID: 238315  Cd Length: 102  Bit Score: 33.76  E-value: 3.89e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 2570276357  36 VHLGVEVLICGGISNFLYHQLVARGIQVIP-WVTGDVEEVLQAYL 79
Cdd:cd00562    58 ALEGCDAVLVGGIGGPAAAKLEAAGIKPIKaAEGGTIEEALEALQ 102
GDPD_GDE1 cd08573
Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester ...
 38-84 4.93e-03

Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE1 and similar proteins; This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE1 (also known as MIR16, membrane interacting protein of RGS16) and their metazoan homologs. GDE1 is widely expressed in mammalian tissues, including the heart, brain, liver, and kidney. It shows sequence homology to bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. GDE1 has been characterized as GPI-GDE (EC 3.1.4.44) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate glycerol phosphate and inositol. It functions as an integral membrane-bound glycoprotein interacting with regulator of G protein signaling protein RGS16, and is modulated by G protein-coupled receptor (GPCR) signaling. In addition, GDE1 may interact with PRA1 domain family, member 2 (PRAF2, also known as JM4), which is an interacting protein of the G protein-coupled chemokine receptor CCR5. The catalytic activity, which is dependent on the integrity of the GDPD domain, is required for GDE1 cellular function.


Pssm-ID: 176515 [Multi-domain]  Cd Length: 258  Bit Score: 34.54  E-value: 4.93e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2570276357  38 LGVEVLICGG--ISNFLYHQLVARGIQVIPWVTGDVEEvlQAYLQDQLN 84
Cdd:cd08573   204 LGVSALLIHKddISSAYVRYWRARGIRVIAWTVNTPTE--KQYFAKTLN 250
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH