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8  structures 21  species 0  interactions 25  sequences 1  architecture

Family: PTase_Orf2 (PF11468)

Summary: Aromatic prenyltransferase Orf2

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This is the Wikipedia entry entitled "Pt-barrel". More...

Pt-barrel Edit Wikipedia article

Orf2-like Prenyltransferase
Orf2 anim1X.gif
Crystal structure of a PT-barrel protein.
Identifiers
Symbol PTase_Orf2
Pfam PF11468
InterPro IPR020965
SCOP 1zb6
SUPERFAMILY 1zb6

The PT-barrel, is a novel protein fold that was discovered in the crystal structure of the prenyltransferase, Orf2 from Streptomyces sp. strain CL190.[1]

Structure[edit]

The PT-barrel consists of a closed β-sheet comprising ten anti-parallel β-strands arranged around a central β-barrel core, itself surrounded by a ring of α-helices forming the outer, solvent exposed surface of the barrel.

The secondary connectivity nearly conforms to an (ααββ)5 classification, but is more specifically described using the (ααββ)4-(αββ)−α nomenclature, where helices 6 and 8, both involved in inter-protein contacts in the crystal lattice, display a helical “kink”. The most hydrophobic section of the PT-barrel is the region residing between the outer surface of the cylindrical β-barrel and the belt of surrounding α-helices. Additionally, a number of hydrophobic residues located inside the barrel accommodate the prenyl tail of the Geranyl-diPhosphate (GPP) and GSPP molecules, while the diphosphate or the thio-diphosphate head groups of substrate and substrate analogs, respectively, point toward the “upper”, more polar end of the barrel where a Mg2+ ion is coordinated. Finally, the bottom of the barrel is capped by a short C-terminal helix (α11).

References[edit]

Press Releases[edit]

Promiscuous Catalytic Activity Possessed by Novel Enzyme Structure, June 15, 2005
SSRL Science Highlight July 2005
LightSource.org Press Release Number: PR-SSRL-05-3

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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.

Aromatic prenyltransferase Orf2 Provide feedback

In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis [1]. In vitro, Orf2 catalyses carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin [1].

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR020965

This entry represents an aromatic prenyltransferase encoded by Orf2 from Streptomyces sp. strain CL190 [PUBMED:15959519]. In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis [PUBMED:15959519]. In vitro, Orf2 catalyses carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin [PUBMED:15959519].

Domain organisation

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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 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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(12)
Full
(25)
Representative proteomes NCBI
(28)
Meta
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(2)
RP35
(4)
RP55
(7)
RP75
(8)
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  Seed
(12)
Full
(25)
Representative proteomes NCBI
(28)
Meta
(0)
RP15
(2)
RP35
(4)
RP55
(7)
RP75
(8)
Alignment:
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  Seed
(12)
Full
(25)
Representative proteomes NCBI
(28)
Meta
(0)
RP15
(2)
RP35
(4)
RP55
(7)
RP75
(8)
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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:

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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.

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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.

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Seed source: pdb_1zb6
Previous IDs: none
Type: Family
Author: Pollington J
Number in seed: 12
Number in full: 25
Average length of the domain: 292.20 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 93.44 %

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 22.0 22.0
Trusted cut-off 175.7 175.4
Noise cut-off 21.4 20.9
Model length: 293
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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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 PTase_Orf2 domain has been found. There are 8 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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