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423  structures 8355  species 0  interactions 40156  sequences 285  architectures

Family: 2-Hacid_dh (PF00389)

Summary: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain Provide feedback

This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain.

Literature references

  1. Dengler U, Niefind K, Kiess M, Schomburg D; , J Mol Biol 1997;267:640-660.: Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. PUBMED:9126843 EPMC:9126843


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006139

A number of NAD-dependent 2-hydroxyacid dehydrogenases which seem to be specific for the D-isomer of their substrate have been shown to be functionally and structurally related. The catalytic domain contains a number of conserved charged residues which may play a role in the catalytic mechanism [ PUBMED:9126843 ]. The NAD-binding domain is described in INTERPRO .

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Form_Glyc_dh (CL0325), which has the following description:

This superfamily includes the catalytic domain of a variety of dehydrogenase enzymes. The domain has a flavodoxin-like fold and contains an inserted Rossman fold NAD-binding domain.

The clan contains the following 4 members:

2-Hacid_dh AdoHcyase AlaDh_PNT_N DpaA_N

Alignments

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 and the UniProtKB sequence database. More...

View options

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
(78)
Full
(40156)
Representative proteomes UniProt
(165316)
RP15
(4722)
RP35
(17941)
RP55
(38077)
RP75
(65431)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(78)
Full
(40156)
Representative proteomes UniProt
(165316)
RP15
(4722)
RP35
(17941)
RP55
(38077)
RP75
(65431)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(78)
Full
(40156)
Representative proteomes UniProt
(165316)
RP15
(4722)
RP35
(17941)
RP55
(38077)
RP75
(65431)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: Prosite
Previous IDs: 2-Hacid_DH;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 78
Number in full: 40156
Average length of the domain: 306.30 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 81.64 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null --hand HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.6 24.6
Trusted cut-off 24.6 24.6
Noise cut-off 24.5 24.5
Model length: 134
Family (HMM) version: 32
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 2-Hacid_dh domain has been found. There are 423 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0WZL3 View 3D Structure Click here
A0A0P0X499 View 3D Structure Click here
A0A0P0X8A3 View 3D Structure Click here
A0A0P0XGH5 View 3D Structure Click here
A0A1D6DW07 View 3D Structure Click here
A0A1D6EFG1 View 3D Structure Click here
A0A1D6ENC3 View 3D Structure Click here
A0A1D6F1R2 View 3D Structure Click here
A0A1D6FZH4 View 3D Structure Click here
A0A1D6GXQ6 View 3D Structure Click here
A0A1D6J2N4 View 3D Structure Click here
A0A1D6KCW2 View 3D Structure Click here
A0A1D6KNM8 View 3D Structure Click here
A0A1D6L0I3 View 3D Structure Click here
A0A1D6QTI4 View 3D Structure Click here
A0A1D8PCW3 View 3D Structure Click here
A0A1D8PI81 View 3D Structure Click here
A0A1D8PNS1 View 3D Structure Click here
A0A2R8QBA1 View 3D Structure Click here
B0BN46 View 3D Structure Click here
B0M1A3 View 3D Structure Click here
B4FA28 View 3D Structure Click here
B4G011 View 3D Structure Click here
B6SLR7 View 3D Structure Click here
C0P848 View 3D Structure Click here
C0PLN9 View 3D Structure Click here
C6T9Z5 View 3D Structure Click here
E9AG23 View 3D Structure Click here
F1QEY8 View 3D Structure Click here
F1QW85 View 3D Structure Click here
F1QYH7 View 3D Structure Click here
F4IBQ3 View 3D Structure Click here
I1KG47 View 3D Structure Click here
I1KGN9 View 3D Structure Click here
I1KIL1 View 3D Structure Click here
I1KVS6 View 3D Structure Click here
I1LEI9 View 3D Structure Click here
I1M611 View 3D Structure Click here
I1MCQ6 View 3D Structure Click here
I1N5R9 View 3D Structure Click here
I1N5S0 View 3D Structure Click here
I1NFX7 View 3D Structure Click here
I6WZ71 View 3D Structure Click here
K7KCB6 View 3D Structure Click here
K7KJD2 View 3D Structure Click here
K7L0E3 View 3D Structure Click here
K7L0E4 View 3D Structure Click here
K7L0E7 View 3D Structure Click here
K7U1Y7 View 3D Structure Click here
O04130 View 3D Structure Click here
O08651 View 3D Structure Click here
O14075 View 3D Structure Click here
O17626 View 3D Structure Click here
O43175 View 3D Structure Click here
O46036 View 3D Structure Click here
O49485 View 3D Structure Click here
O88712 View 3D Structure Click here
O94574 View 3D Structure Click here
P05459 View 3D Structure Click here
P0A9T0 View 3D Structure Click here
P37666 View 3D Structure Click here
P40054 View 3D Structure Click here
P40510 View 3D Structure Click here
P52643 View 3D Structure Click here
P53839 View 3D Structure Click here
P56545 View 3D Structure Click here
P56546 View 3D Structure Click here
P87228 View 3D Structure Click here
P9WNX3 View 3D Structure Click here
Q08911 View 3D Structure Click here
Q0D7C9 View 3D Structure Click here
Q0JFF8 View 3D Structure Click here
Q13363 View 3D Structure Click here
Q1RLQ4 View 3D Structure Click here
Q20595 View 3D Structure Click here
Q2FV62 View 3D Structure Click here
Q2FVA3 View 3D Structure Click here
Q2FVW4 View 3D Structure Click here
Q2FXK1 View 3D Structure Click here
Q2FZW9 View 3D Structure Click here
Q2G1I1 View 3D Structure Click here
Q2G281 View 3D Structure Click here
Q54DP1 View 3D Structure Click here
Q54UF7 View 3D Structure Click here
Q54UH8 View 3D Structure Click here
Q58424 View 3D Structure Click here
Q59P08 View 3D Structure Click here
Q59QN6 View 3D Structure Click here
Q59SC0 View 3D Structure Click here
Q5A3K7 View 3D Structure Click here
Q5ALV4 View 3D Structure Click here
Q5N7Y9 View 3D Structure Click here
Q61753 View 3D Structure Click here
Q67U69 View 3D Structure Click here
Q67Y01 View 3D Structure Click here
Q6YU90 View 3D Structure Click here
Q6ZAA5 View 3D Structure Click here
Q7SZY8 View 3D Structure Click here
Q7X6P0 View 3D Structure Click here
Q7XMP6 View 3D Structure Click here
Q7XRA2 View 3D Structure Click here
Q7XRA3 View 3D Structure Click here
Q84L66 View 3D Structure Click here
Q8I725 View 3D Structure Click here
Q8INU6 View 3D Structure Click here
Q8SZU0 View 3D Structure Click here
Q91Z53 View 3D Structure Click here
Q9C9W5 View 3D Structure Click here
Q9CA90 View 3D Structure Click here
Q9DEG7 View 3D Structure Click here
Q9EQH5 View 3D Structure Click here
Q9LE33 View 3D Structure Click here
Q9LT69 View 3D Structure Click here
Q9P7P8 View 3D Structure Click here
Q9P7Q1 View 3D Structure Click here
Q9S7E4 View 3D Structure Click here
Q9SXP2 View 3D Structure Click here
Q9UBQ7 View 3D Structure Click here
Q9VII9 View 3D Structure Click here
Q9VKI8 View 3D Structure Click here
Q9Z2F5 View 3D Structure Click here