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970  structures 7661  species 0  interactions 17205  sequences 131  architectures

Family: Ldh_1_C (PF02866)

Summary: lactate/malate dehydrogenase, alpha/beta C-terminal 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.

lactate/malate dehydrogenase, alpha/beta C-terminal domain Provide feedback

L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate. The enzyme participates in the citric acid cycle. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes.

Literature references

  1. Chapman AD, Cortes A, Dafforn TR, Clarke AR, Brady RL; , J Mol Biol 1999;285:703-712.: Structural basis of substrate specificity in malate dehydrogenases: crystal structure of a ternary complex of porcine cytoplasmic malate dehydrogenase, alpha-ketomalonate and tetrahydoNAD. PUBMED:10075524 EPMC:10075524


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022383

L-lactate dehydrogenases are metabolic enzymes which catalyse the conversion of L-lactate to pyruvate, the last step in anaerobic glycolysis [ PUBMED:11276087 ]. L-lactate dehydrogenase is also found as a lens crystallin in bird and crocodile eyes. L-2-hydroxyisocaproate dehydrogenases are also members of the family. Malate dehydrogenases catalyse the interconversion of malate to oxaloacetate [ PUBMED:8117664 ]. The enzyme participates in the citric acid cycle.

This entry represents the C-terminal, and is thought to be an is an unusual alpha+beta fold.

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 LDH_C (CL0341), which has the following description:

This superfamily includes the C-terminal domain of lactate/malate dehydrogenase as well as the C-terminal domain of the glycosyl hydrolase 4 family.

The clan contains the following 2 members:

Glyco_hydro_4C Ldh_1_C

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
(15)
Full
(17205)
Representative proteomes UniProt
(62868)
RP15
(2514)
RP35
(7960)
RP55
(15539)
RP75
(24393)
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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
(15)
Full
(17205)
Representative proteomes UniProt
(62868)
RP15
(2514)
RP35
(7960)
RP55
(15539)
RP75
(24393)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(15)
Full
(17205)
Representative proteomes UniProt
(62868)
RP15
(2514)
RP35
(7960)
RP55
(15539)
RP75
(24393)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Overington enriched
Previous IDs: ldh_C;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Eddy SR , Griffiths-Jones SR
Number in seed: 15
Number in full: 17205
Average length of the domain: 163.30 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 49.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.6 22.6
Trusted cut-off 22.6 22.6
Noise cut-off 22.5 22.5
Model length: 167
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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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 Ldh_1_C domain has been found. There are 970 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
A0A0R0HKH4 View 3D Structure Click here
A0A0R0HW29 View 3D Structure Click here
A0A0R0J220 View 3D Structure Click here
A0A0R0JRB0 View 3D Structure Click here
A0A0R4J2L9 View 3D Structure Click here
A0A1D6E409 View 3D Structure Click here
A0A1D6FKV9 View 3D Structure Click here
A0A1D6FW04 View 3D Structure Click here
A0A1D6GPH0 View 3D Structure Click here
A0A1D6HWW8 View 3D Structure Click here
A0A1D6IKH4 View 3D Structure Click here
A0A1D6L6A9 View 3D Structure Click here
A0A1D6LZQ3 View 3D Structure Click here
A0A2R9YJL1 View 3D Structure Click here
A1Z9F8 View 3D Structure Click here
A4HY91 View 3D Structure Click here
A4I421 View 3D Structure Click here
A4I9I2 View 3D Structure Click here
A4I9I3 View 3D Structure Click here
A4I9I4 View 3D Structure Click here
A4I9I5 View 3D Structure Click here
B4FEG4 View 3D Structure Click here
B4FFV3 View 3D Structure Click here
B4FG53 View 3D Structure Click here
B4FRJ1 View 3D Structure Click here
B4FZU8 View 3D Structure Click here
B4FZW5 View 3D Structure Click here
B6T856 View 3D Structure Click here
C0PFW3 View 3D Structure Click here
C6KT25 View 3D Structure Click here
C6TGD9 View 3D Structure Click here
C6TM03 View 3D Structure Click here
F1M0M3 View 3D Structure Click here
H2D5S3 View 3D Structure Click here
I1J9W9 View 3D Structure Click here
I1JZP0 View 3D Structure Click here
I1KDM8 View 3D Structure Click here
I1KQU5 View 3D Structure Click here
I1LH25 View 3D Structure Click here
I1LXZ7 View 3D Structure Click here
I1MUZ7 View 3D Structure Click here
K7K4T0 View 3D Structure Click here
K7N4G1 View 3D Structure Click here
O02640 View 3D Structure Click here
O23569 View 3D Structure Click here
O82399 View 3D Structure Click here
O88989 View 3D Structure Click here
P00338 View 3D Structure Click here
P00342 View 3D Structure Click here
P04636 View 3D Structure Click here
P04642 View 3D Structure Click here
P06151 View 3D Structure Click here
P07195 View 3D Structure Click here
P07864 View 3D Structure Click here
P08249 View 3D Structure Click here
P14152 View 3D Structure Click here
P15719 View 3D Structure Click here
P16125 View 3D Structure Click here
P17505 View 3D Structure Click here
P19629 View 3D Structure Click here
P22133 View 3D Structure Click here
P29038 View 3D Structure Click here
P32419 View 3D Structure Click here
P37228 View 3D Structure Click here
P40925 View 3D Structure Click here
P40926 View 3D Structure Click here
P42123 View 3D Structure Click here
P57106 View 3D Structure Click here
P61889 View 3D Structure Click here
P83778 View 3D Structure Click here
P93819 View 3D Structure Click here
P9WK13 View 3D Structure Click here
Q08062 View 3D Structure Click here
Q08BZ4 View 3D Structure Click here
Q0E4Q5 View 3D Structure Click here
Q0J5H3 View 3D Structure Click here
Q27888 View 3D Structure Click here
Q2G1Y5 View 3D Structure Click here
Q2G218 View 3D Structure Click here
Q3U1V6 View 3D Structure Click here
Q42972 View 3D Structure Click here
Q4CTR7 View 3D Structure Click here
Q4D123 View 3D Structure Click here
Q4D4A0 View 3D Structure Click here
Q4D4A1 View 3D Structure Click here
Q4D4A1 View 3D Structure Click here
Q4DDK8 View 3D Structure Click here
Q4DRD8 View 3D Structure Click here
Q4DXL5 View 3D Structure Click here
Q54D04 View 3D Structure Click here
Q54GE6 View 3D Structure Click here
Q54VM2 View 3D Structure Click here
Q5A5S6 View 3D Structure Click here
Q5AMP4 View 3D Structure Click here
Q5QLS8 View 3D Structure Click here
Q60176 View 3D Structure Click here
Q6DBY5 View 3D Structure Click here
Q6DGK2 View 3D Structure Click here
Q6F361 View 3D Structure Click here
Q6YYW3 View 3D Structure Click here
Q6ZMR3 View 3D Structure Click here
Q76NM3 View 3D Structure Click here
Q7FAT9 View 3D Structure Click here
Q7T334 View 3D Structure Click here
Q7XDC8 View 3D Structure Click here
Q7XZW5 View 3D Structure Click here
Q8BVP2 View 3D Structure Click here
Q8H1E2 View 3D Structure Click here
Q8H4E0 View 3D Structure Click here
Q8IE66 View 3D Structure Click here
Q8IX04 View 3D Structure Click here
Q94JA2 View 3D Structure Click here
Q95028 View 3D Structure Click here
Q9BYZ2 View 3D Structure Click here
Q9FJU0 View 3D Structure Click here
Q9LKA3 View 3D Structure Click here
Q9LWZ6 View 3D Structure Click here
Q9P7P7 View 3D Structure Click here
Q9PVK4 View 3D Structure Click here
Q9PVK5 View 3D Structure Click here
Q9SN86 View 3D Structure Click here
Q9SPB8 View 3D Structure Click here
Q9UAV5 View 3D Structure Click here
Q9VEB1 View 3D Structure Click here
Q9VKX2 View 3D Structure Click here
Q9VU28 View 3D Structure Click here
Q9VU29 View 3D Structure Click here
Q9Y7R8 View 3D Structure Click here
Q9ZP05 View 3D Structure Click here
Q9ZP06 View 3D Structure Click here