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357  structures 460  species 6  interactions 655  sequences 13  architectures

Family: RuBisCO_large_N (PF02788)

Summary: Ribulose bisphosphate carboxylase large chain, N-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.

Ribulose bisphosphate carboxylase large chain, N-terminal domain Provide feedback

The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.

Literature references

  1. Taylor TC, Andersson I; , J Mol Biol 1997;265:432-444.: The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate. PUBMED:9034362 EPMC:9034362


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR017443

Ribulose bisphosphate carboxylase (RuBisCO) [PUBMED:6351728, PUBMED:12221984] catalyses the initial step in Calvin's reductive pentose phosphate cycle in plants as well as purple and green bacteria. It consists of a large catalytic unit and a small subunit of undetermined function. In plants, the large subunit is coded by the chloroplast genome while the small subunit is encoded in the nuclear genome. Molecular activation of RuBisCO by CO2 involves the formation of a carbamate with the epsilon-amino group of a conserved lysine residue. This carbamate is stabilised by a magnesium ion. One of the ligands of the magnesium ion is an aspartic acid residue close to the active site lysine [PUBMED:1969412].

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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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, the UniProtKB sequence database, 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
(40)
Full
(655)
Representative proteomes UniProt
(90116)
NCBI
(70711)
Meta
(224)
RP15
(171)
RP35
(512)
RP55
(829)
RP75
(1212)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(40)
Full
(655)
Representative proteomes UniProt
(90116)
NCBI
(70711)
Meta
(224)
RP15
(171)
RP35
(512)
RP55
(829)
RP75
(1212)
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
(40)
Full
(655)
Representative proteomes UniProt
(90116)
NCBI
(70711)
Meta
(224)
RP15
(171)
RP35
(512)
RP55
(829)
RP75
(1212)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Sonnhammer ELL, Griffiths-Jones SR
Number in seed: 40
Number in full: 655
Average length of the domain: 113.70 aa
Average identity of full alignment: 38 %
Average coverage of the sequence by the domain: 27.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.7 15.0
Trusted cut-off 20.7 17.0
Noise cut-off 20.6 14.8
Model length: 120
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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Interactions

There are 6 interactions for this family. More...

RuBisCO_large RuBisCO_large_N RuBisCO_large RuBisCO_small RcbX RuBisCO_small

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 RuBisCO_large_N domain has been found. There are 357 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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