NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|10835656|pdb|1DLW|A]
View 

Chain A, HEMOGLOBIN

Protein Classification

group I truncated hemoglobin( domain architecture ID 10087425)

group I truncated hemoglobin forms a very stable complex with oxygen; similar to Tetrahymena thermophila group 1 truncated hemoglobin

CATH:  1.10.490.10
Gene Ontology:  GO:0019825|GO:0020037|GO:0005344|GO:0046872
PubMed:  32863222|16061809|19281958|26788940|11696555
SCOP:  3000554

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
TrHb1_N cd00454
truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit ...
 4-114 6.72e-42

truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. It includes a Mycobacterium tuberculosis TrHb1, Mt-trHbN, which is encoded by the glbN gene. Mt-trHbN is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. The cyanobacterium Synechococcus sp. PCC 7002 TrHb1 GlbN, is constitutively expressed, and likely also protects cells from reactive nitrogen species.


:

Pssm-ID: 381253  Cd Length: 111  Bit Score: 133.82  E-value: 6.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        4 EQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTTVIG 83
Cdd:cd00454   1 ERLGGEEGIEAVVDDFYDRVLADPRIKPFFAGVDMARLKKKQTEFLCEAFGGPCEYTGRDMKEAHAGLNITDEHFDAFVE 80

                        90       100       110
                ....*....|....*....|....*....|.
1DLW_A       84 HLRSALTGAGVAAALVEQTVAVAETVRGDVV 114
Cdd:cd00454  81 HLKEALEELGVPEELIDEVLAILEPLRPDIV 111
 
Name Accession Description Interval E-value
TrHb1_N cd00454
truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit ...
 4-114 6.72e-42

truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. It includes a Mycobacterium tuberculosis TrHb1, Mt-trHbN, which is encoded by the glbN gene. Mt-trHbN is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. The cyanobacterium Synechococcus sp. PCC 7002 TrHb1 GlbN, is constitutively expressed, and likely also protects cells from reactive nitrogen species.


Pssm-ID: 381253  Cd Length: 111  Bit Score: 133.82  E-value: 6.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        4 EQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTTVIG 83
Cdd:cd00454   1 ERLGGEEGIEAVVDDFYDRVLADPRIKPFFAGVDMARLKKKQTEFLCEAFGGPCEYTGRDMKEAHAGLNITDEHFDAFVE 80

                        90       100       110
                ....*....|....*....|....*....|.
1DLW_A       84 HLRSALTGAGVAAALVEQTVAVAETVRGDVV 114
Cdd:cd00454  81 HLKEALEELGVPEELIDEVLAILEPLRPDIV 111
YjbI COG2346
Truncated hemoglobin YjbI [Inorganic ion transport and metabolism];
1-115 7.90e-32

Truncated hemoglobin YjbI [Inorganic ion transport and metabolism];


Pssm-ID: 441915  Cd Length: 120  Bit Score: 108.42  E-value: 7.90e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        1 SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTT 80
Cdd:COG2346   5 TLYERIGGEEAIRALVDRFYDRVRADPLLGPIFPEADLEEHREKLADFLSQVLGGPGLYSGRRMRARHAPLPITEEHFDR 84

                        90       100       110
                ....*....|....*....|....*....|....*
1DLW_A       81 VIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVT 115
Cdd:COG2346  85 WLELMREALDELGVPPELAEELLARLERIADDMVN 119
Bac_globin pfam01152
Bacterial-like globin; This family of heme binding proteins are found mainly in bacteria. ...
 1-113 7.86e-17

Bacterial-like globin; This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well.


Pssm-ID: 395917  Cd Length: 121  Bit Score: 70.13  E-value: 7.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A          1 SLFEQLGGQAAVQAVTAQFYANIQADATVA--TFFNGIDMPNQTNKTAAFLCAALGGPNAWTGR----NLKEVHANMGVS 74
Cdd:pfam01152   1 TLYDAIGGEATVRALVDRFYTRVDTDPEEAlsRAFHGTDLEGSRQKLYEFLVQWLGGPPLYSQRrghpRLRGRHAPFPIT 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
1DLW_A         75 NAQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDV 113
Cdd:pfam01152  81 HRERDAWLRHMARAMADTGVHSIDREIILKLMTFLAHTA 119
 
Name Accession Description Interval E-value
TrHb1_N cd00454
truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit ...
 4-114 6.72e-42

truncated hemoglobins (TrHbs, 2/2Hb, 2/2 globins); group 1 (N); The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. It includes a Mycobacterium tuberculosis TrHb1, Mt-trHbN, which is encoded by the glbN gene. Mt-trHbN is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. The cyanobacterium Synechococcus sp. PCC 7002 TrHb1 GlbN, is constitutively expressed, and likely also protects cells from reactive nitrogen species.


Pssm-ID: 381253  Cd Length: 111  Bit Score: 133.82  E-value: 6.72e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        4 EQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTTVIG 83
Cdd:cd00454   1 ERLGGEEGIEAVVDDFYDRVLADPRIKPFFAGVDMARLKKKQTEFLCEAFGGPCEYTGRDMKEAHAGLNITDEHFDAFVE 80

                        90       100       110
                ....*....|....*....|....*....|.
1DLW_A       84 HLRSALTGAGVAAALVEQTVAVAETVRGDVV 114
Cdd:cd00454  81 HLKEALEELGVPEELIDEVLAILEPLRPDIV 111
YjbI COG2346
Truncated hemoglobin YjbI [Inorganic ion transport and metabolism];
1-115 7.90e-32

Truncated hemoglobin YjbI [Inorganic ion transport and metabolism];


Pssm-ID: 441915  Cd Length: 120  Bit Score: 108.42  E-value: 7.90e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        1 SLFEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTT 80
Cdd:COG2346   5 TLYERIGGEEAIRALVDRFYDRVRADPLLGPIFPEADLEEHREKLADFLSQVLGGPGLYSGRRMRARHAPLPITEEHFDR 84

                        90       100       110
                ....*....|....*....|....*....|....*
1DLW_A       81 VIGHLRSALTGAGVAAALVEQTVAVAETVRGDVVT 115
Cdd:COG2346  85 WLELMREALDELGVPPELAEELLARLERIADDMVN 119
TrHb cd14756
Truncated Mb-fold globins, T family; The M- and S families exhibit the canonical secondary ...
 4-114 7.08e-30

Truncated Mb-fold globins, T family; The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. They are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). Typical of the TrHb1s (N) group is a protein matrix tunnel. An example of a TrHb1 is Mycobacterium tuberculosis TrHb1/Mt-trHbN which is expressed during the Mycobacterium stationary phase, and plays a specific defense role against nitrosative stress. TrHb2s include the dimeric Arabidopsis thaliana TrHb2 AtGLB3. GLB3 is likely to have a function distinct from other plant globins: it exhibits a low O2 affinity, an unusual concentration-independent binding of O2 and CO, and does not respond to any of the treatments that induce plant 3-on-3 globins. TrHb3s include Campylobacter jejuni Ctb, encoded by Cj0465c, which may play a role in moderating O2 flux within C. jejuni.


Pssm-ID: 381270 [Multi-domain]  Cd Length: 111  Bit Score: 103.26  E-value: 7.08e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        4 EQLGGQAAVQAVTAQFYANIQADATVATFFNGIDMPNQTNKTAAFLCAALGGPNAWTGRNLKEVHANMGVSNAQFTTVIG 83
Cdd:cd14756   1 EKIGGEEAIEALVEIFYEKVLADPRLKPIFPNTDMKEHKAKQGDFLAGYLGGPNDHGGPMMRRRHLGLPITNEHFDAWLS 80

                        90       100       110
                ....*....|....*....|....*....|.
1DLW_A       84 HLRSALTGAGVAAALVEQTVAVAETVRGDVV 114
Cdd:cd14756  81 LLADALDEVGVNPEMRNEILAVIEMTARHMQ 111
Bac_globin pfam01152
Bacterial-like globin; This family of heme binding proteins are found mainly in bacteria. ...
 1-113 7.86e-17

Bacterial-like globin; This family of heme binding proteins are found mainly in bacteria. However they can also be found in some protozoa and plants as well.


Pssm-ID: 395917  Cd Length: 121  Bit Score: 70.13  E-value: 7.86e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A          1 SLFEQLGGQAAVQAVTAQFYANIQADATVA--TFFNGIDMPNQTNKTAAFLCAALGGPNAWTGR----NLKEVHANMGVS 74
Cdd:pfam01152   1 TLYDAIGGEATVRALVDRFYTRVDTDPEEAlsRAFHGTDLEGSRQKLYEFLVQWLGGPPLYSQRrghpRLRGRHAPFPIT 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
1DLW_A         75 NAQFTTVIGHLRSALTGAGVAAALVEQTVAVAETVRGDV 113
Cdd:pfam01152  81 HRERDAWLRHMARAMADTGVHSIDREIILKLMTFLAHTA 119
TrHb2_O-like cd14775
Truncated hemoglobins, group 2 (O); uncharacterized subgroup; The M- and S families exhibit ...
 3-77 1.04e-06

Truncated hemoglobins, group 2 (O); uncharacterized subgroup; The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P).


Pssm-ID: 381284  Cd Length: 119  Bit Score: 44.16  E-value: 1.04e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A        3 FEQLGGQAAVQAVTAQFYANIQADATVATFFNGIDmPNQTNKTAAFLCAALGGPNAWTGR-----NLKEVHANMGVSNAQ 77
Cdd:cd14775   1 YEWAGGEEALRRLTEAFYARVLADPLLAPVFAHMS-PDHVEHVAAFLAEVFGGPARYTDElggheHMLRHHAGLGITEEQ 79
Globin-like cd01067
Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety ...
 10-94 5.89e-05

Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety of all-helical proteins that bind porphyrins, phycobilins, and other non-heme cofactors, and play various roles in all three kingdoms of life, including sensors or transporters of oxygen. It includes the M/myoglobin-like, S/sensor globin, and T/truncated globin (TrHb) families, and the phycobiliproteins (PBPs). The M family includes chimeric (FHbs/flavohemoglobins) and single-domain globins: FHbs, Ngbs/neuroglobins, Cygb/cytoglobins, GbE/avian eye specific globin E, GbX/globin X, amphibian GbY/globin Y, Mb/myoglobin, HbA/hemoglobin-alpha, HbB/hemoglobin-beta, SDgbs/single-domain globins related to FHbs, and Adgb/androglobin. The S family includes GCS/globin-coupled sensors, Pgbs/protoglobins, and SSDgbs/sensor single domain globins. The T family is classified into three main groups: TrHb1s (N), TrHb2s (O) and TrHb3s (P). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments (named A through H). For M family Adgbs, this globin domain is permuted, such that C-H are followed by A-B. The T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. PBPs bind the linear tetrapyrrole chromophore, phycobilin, a prosthetic group chemically and metabolically related to iron protoporphyrin IX/protoheme. Examples of other globin-like domains which bind non-heme cofactors include those of the Bacillus anthracis sporulation inhibitors pXO1-118 and pXO2-61 which bind fatty acid and halide in vitro, and the globin-like domain of Bacillus subtilis RsbRA which is presumed to channel sensory input to the C-terminal sulfate transporter/ anti-sigma factor antagonist (STAT) domain. RsbRA is a component of the sigma B-activating stressosome, and a regulator of the RNA polymerase sigma factor subunit sigma (B).


Pssm-ID: 381255 [Multi-domain]  Cd Length: 119  Bit Score: 39.36  E-value: 5.89e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1DLW_A       10 AAVQAVTAQFYANIQADATVATFFNGidmPNQTNKTA----AFLCAALGGPNA-----WTGRNLKEVHANMGVSNAQFTT 80
Cdd:cd01067   7 ENQEEIVDDFYDRLFALPSLSELFSP---PGRLAKCIrkqmHFLRYALYGLVDgdsieEGLAGLGEAHKSLGVPISYFIA 83

                        90
                ....*....|....
1DLW_A       81 VIGHLRSALTGAGV 94
Cdd:cd01067  84 ALNVMKDVLTELLG 97
TrHb2_Bs-trHb-like_O cd14772
Truncated hemoglobins, group 2 (O); Bacillus subtilis TrHb like; The M- and S families exhibit ...
 3-60 2.88e-03

Truncated hemoglobins, group 2 (O); Bacillus subtilis TrHb like; The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb2's belonging to this group include monomeric Bacillus subtilis trHb (Bs-trHb), which exhibits an extremely high oxygen affinity, and a dimeric TrHb2 from the thermophilic aerobic spore forming bacterium Geobacillus stearothermophilus(Gs-trHb).


Pssm-ID: 381281  Cd Length: 116  Bit Score: 34.69  E-value: 2.88e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
1DLW_A        3 FEQLGGQAAVQAVTAQFYANIQADATVATFFNGiDMPNQTNKTAAFLCAALGGPNAWT 60
Cdd:cd14772   1 YERIGGEETLSRLVEAFYPRVAAHPLLAPIFPD-DLTETARKQKQFLTQFFGGPPLYT 57
TrHb2_PhHbO-like_O cd14773
Truncated hemoglobins, group 2 (O); Pseudoalteromonas haloplanktis PhHbO like; The M- and S ...
 3-74 7.21e-03

Truncated hemoglobins, group 2 (O); Pseudoalteromonas haloplanktis PhHbO like; The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments. Truncated hemoglobins (TrHbs, 2/2Hb, or 2/2 globins) or the T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. TrHbs are classified into three main groups based on their structural properties and named after Mycobacterium sp. genes glbN, glbO, and glbP: TrHb1s (N), TrHb2s (O) and TrHb3s (P). TrHb2's belonging to this group include Pseudoalteromonas haloplanktis PhHbO (encoded by the PSHAa0030 gene) which appears to be involved in oxidative and nitrosative stress resistance.


Pssm-ID: 381282  Cd Length: 119  Bit Score: 33.67  E-value: 7.21e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1DLW_A        3 FEQLGGQAAVQAVTAQFYANIQADATVATF--FNGIDMPNQTNKTAAFLCAALGGPNAWT----GRNLKEVHANMGVS 74
Cdd:cd14773   1 YERIGGEEGVRALVDRFYDLMDTLPEAAELraMHPDDLTPSREKLFEFLSGWLGGPRLYSekygHPRLRSRHAPFPIG 78
 
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