Summary: Histidine biosynthesis protein
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Histidine biosynthesis protein Provide feedback
Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel e.g. P05325 [3]. This family belong to the common phosphate binding site TIM barrel family [4].
Literature references
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Fani R, Tamburini E, Mori E, Lazcano A, Lio P, Barberio C, Casalone E, Cavalieri D, Perito B, Polsinelli M, , Gene 1997;197:9-17.: Paralogous histidine biosynthetic genes: evolutionary analysis of the Saccharomyces cerevisiae HIS6 and HIS7 genes. PUBMED:9332345 EPMC:9332345
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Fani R, Lio P, Chiarelli I, Bazzicalupo M; , J Mol Evol 1994;38:489-495.: The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. PUBMED:8028028 EPMC:8028028
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Fani R, Lio P, Chiarelli I, Bazzicalupo M; , J Mol Evol 1994;38:489-495.: The evolution of the histidine biosynthetic genes in prokaryotes: a common ancestor for the hisA and hisF genes. PUBMED:8028028 EPMC:8028028
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Copley RR, Bork P; , J Mol Biol 2000;303:627-641.: Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways. PUBMED:11054297 EPMC:11054297
Internal database links
SCOOP: | BtpA CBS DeoC DHO_dh DUF561 Dus F_bP_aldolase FliG_C FliG_M FliG_N FMN_dh G3P_antiterm Glu_synthase IGPS IMPDH MR_MLE_C NanE NMO OMPdecase Oxidored_FMN PcrB PEP_mutase Peripla_BP_6 QRPTase_C Radical_SAM Ribul_P_3_epim SOR_SNZ ThiG TMP-TENI Trp_syntA |
Similarity to PfamA using HHSearch: | IGPS IMPDH Dus Dus PcrB TMP-TENI NMO G3P_antiterm |
External database links
HOMSTRAD: | His_biosynth |
SCOP: | 1thf |
This tab holds annotation information from the InterPro database.
InterPro entry IPR006062
Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in one family. These enzymes are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. HisA is a phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (EC), involved in the fourth step of histidine biosynthesis. The bacterial HisF protein is a cyclase which catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate during the sixth step of histidine biosynthesis. The yeast His7 protein is a bifunctional protein which catalyzes an amido-transferase reaction that generates imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide. The latter is the ribonucleotide used for purine biosynthesis. The enzyme also catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate, and is involved in the fifth and sixth steps in histidine biosynthesis.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Biological process | histidine biosynthetic process (GO:0000105) |
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan TIM_barrel (CL0036), which has the following description:
This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].
The clan contains the following 60 members:
4HFCP_synth Ala_racemase_N ALAD Aldolase AP_endonuc_2 BtpA CdhD ComA CutC DAHP_synth_1 DAHP_synth_2 DeoC DHDPS DHO_dh DHquinase_I DUF2090 DUF4862 DUF561 DUF692 DUF993 Dus F_bP_aldolase FMN_dh G3P_antiterm GatZ_KbaZ-like Glu_syn_central Glu_synthase His_biosynth HMGL-like IGPS IMPDH KDGP_aldolase Lys-AminoMut_A MtrH NanE NAPRTase NeuB NMO OAM_alpha OMPdecase Orn_Arg_deC_N Oxidored_FMN PcrB PdxJ PRAI PRMT5_TIM Pterin_bind QRPTase_C Radical_SAM RhaA Ribul_P_3_epim SOR_SNZ TAL_FSA ThiC_Rad_SAM ThiG TIM TMP-TENI Trp_syntA UvdE UxuAAlignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
Seed (131) |
Full (15123) |
Representative proteomes | UniProt (63746) |
NCBI (95246) |
Meta (6555) |
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RP15 (1980) |
RP35 (7239) |
RP55 (14758) |
RP75 (25150) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (131) |
Full (15123) |
Representative proteomes | UniProt (63746) |
NCBI (95246) |
Meta (6555) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (1980) |
RP35 (7239) |
RP55 (14758) |
RP75 (25150) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
Seed source: | Pfam-B_1089 (release 3.0) |
Previous IDs: | none |
Type: | Family |
Sequence Ontology: | SO:0100021 |
Author: |
Copley RD, Finn RD |
Number in seed: | 131 |
Number in full: | 15123 |
Average length of the domain: | 230.90 aa |
Average identity of full alignment: | 32 % |
Average coverage of the sequence by the domain: | 85.16 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 229 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the His_biosynth domain has been found. There are 88 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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