Summary: Glycine cleavage T-protein C-terminal barrel domain

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Wikipedia: Glycine cleavage system
Pfam
InterPro

This is the Wikipedia entry entitled "Glycine cleavage system". More...

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Glycine cleavage system

Glycine cleavage in the photorespiratory pathway.

Glycine cleavage H-protein

refined structures at 2 angstroms and 2.2 angstroms of the two forms of the h-protein, a lipoamide-containing protein of the glycine decarboxylase

Identifiers

Symbol

GCV_H

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Glycine cleavage T-protein, Aminomethyltransferase folate-binding domain

crystal structure of a component of glycine cleavage system: t-protein from pyrococcus horikoshii ot3 at 1.5 a resolution

Identifiers

Symbol

GCV_T

Pfam clan

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Glycine cleavage T-protein C-terminal barrel domain

crystal structure of t-protein of the glycine cleavage system

Identifiers

Symbol

GCV_T_C

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

The glycine cleavage system is also known as the glycine decarboxylase complex or GCS. The system is a series of enzymes that are triggered in response to high concentrations of the amino acid glycine.^[1] The glycine cleavage system is composed of four proteins: the T-protein, P-protein, L-protein, and H-protein. They do not form a stable complex,^[2] so it is more appropriate to call it a "system" instead of a "complex"

[edit] Components

Name	EC number	Function
T-protein (GCST or AMT)	EC 2.1.2.10	aminomethyltransferase
P-protein (GLDC)	EC 1.4.4.2	glycine dehydrogenase (decarboxylating) or just glycine dehydrogenase.
L-protein (GCSL or DLD)	EC 1.8.1.4	known by many names, but most commonly dihydrolipoyl dehydrogenase
H-protein (GCSH)		is modified with lipoic acid and interacts with all other components in a cycle of reductive methylamination (catalysed by the P-protein), methylamine transfer (catalysed by the T-protein) and electron transfer (catalysed by the L-protein).^[2]

[edit] Function

In plants the glycine cleavage system is coupled to serine hydroxymethyltransferase to give an overall reaction of:

2 glycine + NAD⁺ + H₂O → serine + CO₂ + NH₃ + NADH + H⁺

This reaction, and by extension the glycine cleavage system, is required for photorespiration in C₃ plants. Together the proteins involved in these reactions comprise about half the proteins in mitochondria from spinach and pea leaves.^[2]

[edit] See also

[edit] References

^ Kikuchi G (June 1973). "The glycine cleavage system: composition, reaction mechanism, and physiological significance". Mol. Cell. Biochem. 1 (2): 169–87. doi:10.1007/BF01659328. PMID 4585091.
^ ^a ^b ^c Douce R, Bourguignon J, Neuburger M, Rébeillé F (April 2001). "The glycine decarboxylase system: a fascinating complex". Trends Plant Sci. 6 (4): 167–76. doi:10.1016/S1360-1385(01)01892-1. PMID 11286922.

Metabolism: amino acid metabolism · synthesis and catabolism enzymes (essential in CAPS)

K→acetyl-CoA

LYSINE→	Saccharopine dehydrogenase · Glutaryl-CoA dehydrogenase

LEUCINE→	Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · Isovaleryl coenzyme A dehydrogenase · Methylcrotonyl-CoA carboxylase · Methylglutaconyl-CoA hydratase · 3-hydroxy-3-methylglutaryl-CoA lyase

TRYPTOPHAN→	Indoleamine 2,3-dioxygenase/Tryptophan 2,3-dioxygenase · Arylformamidase · Kynureninase · 3-hydroxyanthranilate oxidase · Aminocarboxymuconate-semialdehyde decarboxylase · Aminomuconate-semialdehyde dehydrogenase

PHENYLALANINE→tyrosine→	(see below)

G

G→pyruvate
→citrate

glycine→serine→	Serine hydroxymethyltransferase · Serine dehydratase glycine→creatine: Guanidinoacetate N-methyltransferase · Creatine kinase

alanine→	Alanine transaminase

cysteine→	D-cysteine desulfhydrase

threonine→	L-threonine dehydrogenase

G→glutamate→
α-ketoglutarate


HISTIDINE→	Histidine ammonia-lyase · Urocanate hydratase · Formiminotransferase cyclodeaminase

proline→	Proline oxidase · Pyrroline-5-carboxylate reductase · 1-Pyrroline-5-carboxylate dehydrogenase/ALDH4A1 · PYCR1

arginine→	Ornithine aminotransferase · Ornithine decarboxylase · Agmatinase

→alpha-ketoglutarate→TCA	Glutamate dehydrogenase

Other	cysteine+glutamate→glutathione: Gamma-glutamylcysteine synthetase · Glutathione synthetase · Gamma-glutamyl transpeptidase glutamate→glutamine: Glutamine synthetase · Glutaminase

G→propionyl-CoA→
succinyl-CoA

VALINE→	Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · Enoyl-CoA hydratase · 3-hydroxyisobutyryl-CoA hydrolase · 3-hydroxyisobutyrate dehydrogenase · Methylmalonate semialdehyde dehydrogenase

ISOLEUCINE→	Branched chain aminotransferase · Branched-chain alpha-keto acid dehydrogenase complex · 3-hydroxy-2-methylbutyryl-CoA dehydrogenase

METHIONINE→	generation of homocysteine: Methionine adenosyltransferase · Adenosylhomocysteinase regeneration of methionine: Methionine synthase/Homocysteine methyltransferase · Betaine-homocysteine methyltransferase conversion to cysteine: Cystathionine beta synthase · Cystathionine gamma-lyase

THREONINE→	Threonine aldolase

→succinyl-CoA→TCA	Propionyl-CoA carboxylase · Methylmalonyl CoA epimerase · Methylmalonyl-CoA mutase

G→fumarate


PHENYLALANINE→tyrosine→	Phenylalanine hydroxylase · Tyrosine aminotransferase · 4-Hydroxyphenylpyruvate dioxygenase · Homogentisate 1,2-dioxygenase · Fumarylacetoacetate hydrolase tyrosine→melanin: Tyrosinase

G→oxaloacetate


asparagine→aspartate→	Asparaginase/Asparagine synthetase · Aspartate transaminase

M: MET

mt, k, c/g/r/p/y/i, f/h/s/l/o/e, a/u, n, m

k, cgrp/y/i, f/h/s/l/o/e, au, n, m, epon

m(A16/C10),i(k, c/g/r/p/y/i, f/h/s/o/e, a/u, n, m)

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Glycine cleavage T-protein C-terminal barrel domain

This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.

Literature references

McNeil JB, Zhang F, Taylor BV, Sinclair DA, Pearlman RE, Bognar AL; , Gene 1997;186:13-20.: Cloning, and molecular characterization of the GCV1 gene encoding the glycine cleavage T-protein from Saccharomyces cerevisiae. PUBMED:9047339

External database links

PANDIT:	PF08669
Pseudofam:	PF08669
SCOP:	1pj5
SYSTERS:	GCV_T_C

This tab holds annotation information from the InterPro database.

InterPro entry IPR013977

This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

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Alignment:	Seed (192) Full (4341) NCBI (3988) Metagenomics (10045)
Viewer:

Formatting options

Alignment:	Seed (192) Full (4341)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (192) Full (4341) NCBI (3988) Metagenomics (10045)
Full length sequences	Full-sequences (4341)

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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_933 (release 4.0)

Previous IDs:

none

Type:

Domain

Author:

Bashton M, Bateman A

Number in seed:

192

Number in full:

4341

Average length of the domain:

94.60 aa

Average identity of full alignment:

25 %

Average coverage of the sequence by the domain:

19.16 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 15929002 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.0	21.0
Trusted cut-off	21.0	21.0
Noise cut-off	20.9	20.9

Model length:

95

Family (HMM) version:

6

Download:

download the raw HMM for this family

Species distribution

Sunburst
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Colour assignments

Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

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 if you need to select sub-trees and view sequence alignments. More...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, it's distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

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Interactions

There are 3 interactions for this family. More...

DAO SoxD GCV_T

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 GCV_T_C domain has been found. There are 15 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 seqence.

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Family: GCV_T_C (PF08669)

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Summary: Glycine cleavage T-protein C-terminal barrel domain

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Glycine cleavage system

Contents

[edit] Components

[edit] Function

[edit] See also

[edit] References

Glycine cleavage T-protein C-terminal barrel domain

Literature references

External database links

InterPro entry IPR013977

Domain organisation

Alignments

Viewing

Downloading

View options

Formatting options

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Interactions

Structures