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36  structures 3935  species 2  interactions 5458  sequences 19  architectures

Family: 6PGD (PF00393)

Summary: 6-phosphogluconate dehydrogenase, C-terminal domain

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This is the Wikipedia entry entitled "Phosphogluconate dehydrogenase". More...

Phosphogluconate dehydrogenase Edit Wikipedia article

6PGD
PDB 1pgq EBI.jpg
Crystallographic structure of sheep 6-phosphogluconate dehydrogenase complexed with adenosine 2'-monophosphate.[1]
Identifiers
Symbol 6PGD
Pfam PF00393
Pfam clan CL0106
InterPro IPR006114
PROSITE PDOC00390
SCOP 2pgd
SUPERFAMILY 2pgd
Phosphogluconate dehydrogenase
Identifiers
EC number 1.1.1.43
CAS number 9001-82-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
phosphogluconate dehydrogenase
Identifiers
Symbol PGD
Entrez 5226
HUGO 8891
OMIM 172200
RefSeq NM_002631
UniProt P52209
Other data
Locus Chr. 1 p36.3-36.13

Phosphogluconate dehydrogenase is an enzyme in the pentose phosphate pathway. It forms ribulose 5-phosphate from 6-phosphogluconate.

It is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP).[2][3] Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequences are highly conserved.[4] The protein is a homodimer in which the monomers act independently:[3] each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet.[3] NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket.[3]

References[edit]

  1. ^ PDB 1PGQ; Adams MJ, Ellis GH, Gover S, Naylor CE, Phillips C (July 1994). "Crystallographic study of coenzyme, coenzyme analogue and substrate binding in 6-phosphogluconate dehydrogenase: implications for NADP specificity and the enzyme mechanism". Structure 2 (7): 651–68. PMID 7922042. 
  2. ^ Broedel SE, Wolf RE (July 1990). "Genetic tagging, cloning, and DNA sequence of the Synechococcus sp. strain PCC 7942 gene (gnd) encoding 6-phosphogluconate dehydrogenase". J. Bacteriol. 172 (7): 4023–31. PMC 213388. PMID 2113917. 
  3. ^ a b c d Adams MJ, Archibald IG, Bugg CE, Carne A, Gover S, Helliwell JR, Pickersgill RW, White SW (1983). "The three dimensional structure of sheep liver 6-phosphogluconate dehydrogenase at 2.6 A resolution". EMBO J. 2 (6): 1009–14. PMC 555222. PMID 6641716. 
  4. ^ Reizer A, Deutscher J, Saier MH, Reizer J (May 1991). "Analysis of the gluconate (gnt) operon of Bacillus subtilis". Mol. Microbiol. 5 (5): 1081–9. doi:10.1111/j.1365-2958.1991.tb01880.x. PMID 1659648. 

This article incorporates text from the public domain Pfam and InterPro IPR006114


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

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6-phosphogluconate dehydrogenase, C-terminal domain Provide feedback

This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006114

6-Phosphogluconate dehydrogenase (EC) (6PGD) is an oxidative carboxylase that catalyses the decarboxylating reduction of 6-phosphogluconate into ribulose 5-phosphate in the presence of NADP. This reaction is a component of the hexose mono-phosphate shunt and pentose phosphate pathways (PPP) [PUBMED:2113917, PUBMED:6641716]. Prokaryotic and eukaryotic 6PGD are proteins of about 470 amino acids whose sequences are highly conserved [PUBMED:1659648]. The protein is a homodimer in which the monomers act independently [PUBMED:6641716]: each contains a large, mainly alpha-helical domain and a smaller beta-alpha-beta domain, containing a mixed parallel and anti-parallel 6-stranded beta sheet [PUBMED:6641716]. NADP is bound in a cleft in the small domain, the substrate binding in an adjacent pocket [PUBMED:6641716].

This entry represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. 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 6PGD_C (CL0106), which has the following description:

This helical domain is found associated with Rossmann domains.

The clan contains the following 6 members:

3HCDH 6PGD IlvC Mannitol_dh_C NAD_Gly3P_dh_C UDPG_MGDP_dh

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
(58)
Full
(5458)
Representative proteomes NCBI
(4118)
Meta
(977)
RP15
(355)
RP35
(715)
RP55
(977)
RP75
(1173)
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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
(58)
Full
(5458)
Representative proteomes NCBI
(4118)
Meta
(977)
RP15
(355)
RP35
(715)
RP55
(977)
RP75
(1173)
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
(58)
Full
(5458)
Representative proteomes NCBI
(4118)
Meta
(977)
RP15
(355)
RP35
(715)
RP55
(977)
RP75
(1173)
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.

Pfam alignments:

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: none
Type: Domain
Author: Finn RD, Griffiths-Jones SR
Number in seed: 58
Number in full: 5458
Average length of the domain: 231.40 aa
Average identity of full alignment: 44 %
Average coverage of the sequence by the domain: 59.81 %

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 20.4 20.4
Trusted cut-off 20.8 20.6
Noise cut-off 19.7 20.3
Model length: 291
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

NAD_binding_2 6PGD

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 6PGD domain has been found. There are 36 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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