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20  structures 3103  species 1  interaction 6351  sequences 14  architectures

Family: GDC-P (PF02347)

Summary: Glycine cleavage system P-protein

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This is the Wikipedia entry entitled "Group I pyridoxal-dependent decarboxylases". More...

Group I pyridoxal-dependent decarboxylases Edit Wikipedia article

Glycine cleavage system P-protein
PDB 1wyt EBI.jpg
crystal structure of glycine decarboxylase (p-protein) of the glycine cleavage system, in apo form
Identifiers
Symbol GDC-P
Pfam PF02347
Pfam clan CL0061
InterPro IPR020580

In molecular biology, the group I pyridoxal-dependent decarboxylases, also known as glycine cleavage system P-proteins, are a family of enzymes consisting of glycine cleavage system P-proteins (glycine dehydrogenase (decarboxylating)) EC 1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T.[1]

Pyridoxal-5'-phosphate-dependent amino acid decarboxylases can be divided into four groups based on amino acid sequence. Group I comprises glycine decarboxylases.[2]

See also[edit]

References[edit]

  1. ^ Stauffer LT, Fogarty SJ, Stauffer GV (May 1994). "Characterization of the Escherichia coli gcv operon". Gene 142 (1): 17–22. doi:10.1016/0378-1119(94)90349-2. PMID 8181752. 
  2. ^ Sandmeier E, Hale TI, Christen P (May 1994). "Multiple evolutionary origin of pyridoxal-5'-phosphate-dependent amino acid decarboxylases". Eur. J. Biochem. 221 (3): 997–1002. doi:10.1111/j.1432-1033.1994.tb18816.x. PMID 8181483. 

This article incorporates text from the public domain Pfam and InterPro IPR020580

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Glycine cleavage system P-protein Provide feedback

This family consists of Glycine cleavage system P-proteins EC:1.4.4.2 from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex EC:2.1.2.10 (GDC) also annotated as glycine cleavage system or glycine synthase. GDC consists of four proteins P, H, L and T [2]. The reaction catalysed by this protein is:- Glycine + lipoylprotein <=> S-aminomethyldihydrolipoylprotein + CO2

Literature references

  1. Sinclair DA, Dawes IW; , Genetics 1995;140:1213-1222.: Genetics of the synthesis of serine from glycine and the utilization of glycine as sole nitrogen source by Saccharomyces cerevisiae. PUBMED:7498764 EPMC:7498764

  2. Stauffer LT, Fogarty SJ, Stauffer GV; , Gene 1994;142:17-22.: Characterization of the Escherichia coli gcv operon. PUBMED:8181752 EPMC:8181752


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020580

This family consists of glycine cleavage system P-proteins (EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T [PUBMED:8181752]. The reaction catalysed by this protein is:

Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2

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 PLP_aminotran (CL0061), which has the following description:

This superfamily contains a variety of PLP-dependent enzymes.

The clan contains the following 15 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SHMT SLA_LP_auto_ag

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(13)
Full
(6351)
Representative proteomes NCBI
(6081)
Meta
(5305)
RP15
(604)
RP35
(1157)
RP55
(1560)
RP75
(1832)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(13)
Full
(6351)
Representative proteomes NCBI
(6081)
Meta
(5305)
RP15
(604)
RP35
(1157)
RP55
(1560)
RP75
(1832)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(13)
Full
(6351)
Representative proteomes NCBI
(6081)
Meta
(5305)
RP15
(604)
RP35
(1157)
RP55
(1560)
RP75
(1832)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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'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: Pfam-B_840 (release 5.2)
Previous IDs: none
Type: Family
Author: Bashton M, Bateman A
Number in seed: 13
Number in full: 6351
Average length of the domain: 362.70 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 75.92 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.8 19.8
Trusted cut-off 19.8 19.8
Noise cut-off 19.7 19.7
Model length: 429
Family (HMM) version: 11
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

GDC-P

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 GDC-P domain has been found. There are 20 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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