LDHB - NM_002300 - network view

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LDHB
NM_002300

You are viewing an updated version (2021) of the ActiveDriverDB. To view the previous version please visit activedriverdb.org/v2020

LDHB (NM_002300) - lactate dehydrogenase B

L-Lactate Dehydrogenase B Chain Isoform Ldhb

Sequence View
Network view, experimental
Network view, MIMP-predicted

Data Filters

Show only the mutations which affect specific PTM sites and/or in specific populations (updates both the Mutations Visualisation plot and table found on the Sequence View tab, and the PTM Interaction Network Visualisation plot found on the Network View tab)

PTM mutations only

Enabling this option will cause the search results to display all mutations (by default, only mutations affecting PTM sites are shown initially)

PTM mutations only

Mutation dataset

This option allows you to select the source of mutation data, which in turn also allows you to select different mutation subsets in the respective submenu (appears once you select the dataset source).

Cancer (TCGA PanCancerAtlas): this exome sequencing dataset allows you to select mutations based on the cancer type in which the mutation was detected. To select specific cancer type(s), de-select “All cancer types”, and then select the cancer type(s) you are interested in – multiple selection can be made.

Clinical (ClinVar): this dataset allows you to select mutations based on their clinical and pathological significance, and disease in which that clinical significance was detected in based on data on the ClinVar database. Selection this option will provide you with two submenus: “Clinical significance” and “Disease name”. To select a specific clinical significance and/or disease, de-select that “All clinical significance” and/or “All disease names” prior to making you selection(s).

Population (ESP6500): this dataset allows you to selected mutations reported in either European American or African American individuals based on exome sequencing of thousands of individuals.

Population (1000 Genomes): Similar to ESP 6500, this genome sequencing dataset allows you to select mutations reported in specific ethnic backgrounds. To select specific ethnic background(s), de-select “All ethnicities” prior to making your selection(s).

Cancer (TCGA PanCancerAtlas)
Cancer (PCAWG)
Clinical (ClinVar)
Population (ESP 6500)
Population (1000 Genomes)

Ethnicity

This filter allows you to select the ethnicity(ies) where mutations of your query protein were observed

(This filter is a sub-filter of the 1000 Genomes mutation dataset selection above)

Any ethnicity
East Asian (EAS)
Ad Mixed American (AMR)
African (AFR)
European (EUR)
South Asian (SAS)

Type of PTM site

This element has no help text defined yet.

Any site
acetylation
glycosylation

C-glycosylation
N-glycosylation
O-glycosylation
S-glycosylation

methylation
phosphorylation

phosphorylation (SARS-CoV-2)

succinylation
sumoylation
ubiquitination

Drug group

This Network View filter option allows you to select the category of kinase-targeting drugs displayed in the network map.

All drug groups
Approved
Experimental
Illicit
Investigational
Nutraceutical
Vet_Approved
Withdrawn

Active

Show sites

This element has no help text defined yet.

Clone kinases by site

This element has no help text defined yet.

Prevent drug overlapping

This element has no help text defined yet.

Legend

Protein

Currently analysed protein

Kinases

Circle: kinases interacting with your protein of interest (centre of the figure) via the specific PTM site as indicated in the network diagram. The colour of the kinase is shaded based on the number of mutations occurring in that kinase.

Octagon: kinase families interacting with your protein of interest (centre of the figure) via the specific PTM site as indicated in the network diagram. The colour of the kinase is shaded based on the number of mutations occurring in that kinase.

Star: drugs predicted to interact with the connected kinase.

Kinase

Group

Drug

Mutations in a kinase:

max

Sites

Mutations affecting PTMs are depicted as square boxes.

PTM Site

Color corresponds to (the most severe) impact of mutations on given site:

direct

network-rewiring

motif-changing

proximal

distal

none

Interactions

Kinase interacts with analysed protein at this site

Loss of interaction predicted

Presence of a connecting line between a mutation and kinase denotes the existence of an interaction at this amino acid location. A dashed red line however denotes that the specific mutation causes a loss of interaction.

If you have any questions or feedback about this protein:

PTM Interaction Network Visualisation

The PTM Interaction Network provides visualization of all PTMs which mediate an interaction between your protein of interest and protein kinases. Each PTM is visualized as a different colour box listing the mutation location and the surrounding amino acid sequence. These PTMs originate from your protein of interest (circle with a dark border) which links it to a kinase (circle with thick border). The colour of the circles corresponds to the number of mutations occurring in the kinase with white being none, and dark blue being a normalized maximum. See figure legend for additional details.

Zooming in/out
If there is a specific PTM you are interested in, you can click on it to zoom onto it and the kinases it has been associated with. Alternatively you can click the magnifying glass icons on the top right of the PTM Interaction Network Visualisation window.

Saving the image
The Interaction Network image can be saved in an SVG or PDF formats by clicking on the “Save image as” button on the top right of the PTM Interaction Network Visualization window.

SVG image
PDF file (print)

Protein summary

The protein summary provides brief information regarding your protein, namely: its full name, a brief description of its function, and genomic location of the coding gene.

This is preferred isoform of LDHB protein. View all 2 isoforms

LDHB: L-lactate dehydrogenase B chain isoform LDHB

Description:

This gene encodes the B subunit of lactate dehydrogenase enzyme, which catalyzes the interconversion of pyruvate and lactate with concomitant interconversion of NADH and NAD+ in a post-glycolysis process. Alternatively spliced transcript variants have been found for this gene. Recent studies have shown that a C-terminally extended isoform is produced by use of an alternative in-frame translation termination codon via a stop codon readthrough mechanism, and that this isoform is localized in the peroxisomes. Mutations in this gene are associated with lactate dehydrogenase B deficiency. Pseudogenes have been identified on chromosomes X, 5 and 13. [provided by RefSeq, Feb 2016].

Strand: -
Chromosome: 12

Protein: 334 residues
All mutations: 50

PTM sites: 40
CDS: 21,788,475 - 21,807,605
Transcription: 21,788,275 - 21,810,789

0.3% of sequence is predicted to be disordered

Usage summary

Network

drag the background to move whole network
scroll to zoom in and out

PTM site

double click to focus on site's sub-network (or hide it)

Kinases group

double click to show/hide all kinases within the group.

Kinase, PTM site or protein

hover to see a tooltip with additional information
click to stick the tooltip
drag a node to move it and stick in a chosen place
shift + click to free a node which was stuck earlier

External references

RefSeq, Entrez, Uniprot and Enzembl IDs related to your search query.

Mappings retrieved from NCBI & UniProt.

RefSeq RefSeq IDs relevant to your search query.

mRNA: NM_002300
protein: NP_002291
gene: NG_017038

Entrez: gene: 3945

UniProt All links following an Uniprot accession refer to this accession. Orange icon ( ) next to an accession indicates that the entry belongs to SwissProt: a reviewed subset of Uniprot knowledgebase. Rarely links to external resources may not work. This is common for new or unreviewed ( ) entries.

P07195
PhosphoSitePlus
PFAM
STRING
phospho3d
Reactome
PDB

Q5U077
PhosphoSitePlus
PFAM
STRING
phospho3d
Reactome
PDB

Ensembl

ENSP00000229319
ENSP00000379386

ReimandLab.org
Ontario Institute for Cancer Research
Licence
Terms of Use
GitHub

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LDHB (NM_002300) - lactate dehydrogenase B

Data Filters Show only the mutations which affect specific PTM sites and/or in specific populations (updates both the Mutations Visualisation plot and table found on the Sequence View tab, and the PTM Interaction Network Visualisation plot found on the Network View tab)

Options

Active

Legend

Protein

Sites Mutations affecting PTMs are depicted as square boxes.

Interactions

Protein summary The protein summary provides brief information regarding your protein, namely: its full name, a brief description of its function, and genomic location of the coding gene.

Usage summary

Network

PTM site

Kinases group

Kinase, PTM site or protein

External references RefSeq, Entrez, Uniprot and Enzembl IDs related to your search query.

Data Filters

Show only the mutations which affect specific PTM sites and/or in specific populations (updates both the Mutations Visualisation plot and table found on the Sequence View tab, and the PTM Interaction Network Visualisation plot found on the Network View tab)

Sites

Mutations affecting PTMs are depicted as square boxes.

Protein summary

The protein summary provides brief information regarding your protein, namely: its full name, a brief description of its function, and genomic location of the coding gene.

External references

RefSeq, Entrez, Uniprot and Enzembl IDs related to your search query.