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9  structures 2351  species 2  interactions 20609  sequences 1841  architectures

Family: Condensation (PF00668)

Summary: Condensation domain

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This is the Wikipedia entry entitled "Condensation domain". More...

Condensation domain Edit Wikipedia article

Condensation
PDB 1l5a EBI.jpg
crystal structure of vibh, an nrps condensation enzyme
Identifiers
Symbol Condensation
Pfam PF00668
Pfam clan CL0149
InterPro IPR001242
SCOP 1l5a
SUPERFAMILY 1l5a

In molecular biology, the condensation domain is a protein domain found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non-ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pp-binding). It has been shown that mutations in the HHXXXDG sequence motif in this domain abolish activity suggesting this is part of the active site.[1]

References[edit]

  1. ^ Stachelhaus T, Mootz HD, Bergendahl V, Marahiel MA (August 1998). "Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain". J. Biol. Chem. 273 (35): 22773–81. PMID 9712910. 

This article incorporates text from the public domain Pfam and InterPro IPR001242

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.

Condensation domain Provide feedback

This domain is found in many multi-domain enzymes which synthesise peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non- ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (PF00550). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site [1].

Literature references

  1. Stachelhaus T, Mootz HD, Bergendahl V, Marahiel MA; , J Biol Chem 1998;273:22773-22781.: Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain. PUBMED:9712910 EPMC:9712910


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001242

This domain is found in many multi-domain enzymes which synthesize peptide antibiotics. This domain catalyses a condensation reaction to form peptide bonds in non-ribosomal peptide biosynthesis. It is usually found to the carboxy side of a phosphopantetheine binding domain (pp-binding). It has been shown that mutations in the HHXXXDG motif abolish activity suggesting this is part of the active site [PUBMED:9712910].

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 CoA-acyltrans (CL0149), which has the following description:

All characterised families in this clan are involved in CoA-dependent acyltransferase. All families have a characteristic HXXXD motif.

The clan contains the following 7 members:

2-oxoacid_dh AATase Carn_acyltransf CAT Condensation Transferase WES_acyltransf

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...

View options

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
(42)
Full
(20609)
Representative proteomes NCBI
(22090)
Meta
(414)
RP15
(1552)
RP35
(3788)
RP55
(5729)
RP75
(7271)
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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
(42)
Full
(20609)
Representative proteomes NCBI
(22090)
Meta
(414)
RP15
(1552)
RP35
(3788)
RP55
(5729)
RP75
(7271)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(42)
Full
(20609)
Representative proteomes NCBI
(22090)
Meta
(414)
RP15
(1552)
RP35
(3788)
RP55
(5729)
RP75
(7271)
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_130 (release 2.1)
Previous IDs: DUF4;
Type: Family
Author: Bateman A
Number in seed: 42
Number in full: 20609
Average length of the domain: 273.20 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 26.78 %

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 20.0 20.0
Trusted cut-off 20.0 20.0
Noise cut-off 19.9 19.9
Model length: 301
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Condensation PP-binding

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 Condensation domain has been found. There are 9 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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