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25  structures 199  species 2  interactions 226  sequences 3  architectures

Family: Lys-AminoMut_A (PF09043)

Summary: D-Lysine 5,6-aminomutase alpha subunit

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This is the Wikipedia entry entitled "D-lysine 5,6-aminomutase". More...

D-lysine 5,6-aminomutase Edit Wikipedia article

D-lysine 5,6-aminomutase
Identifiers
EC number 5.4.3.4
CAS number 9075-70-1
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
D-Lysine 5,6-aminomutase alpha subunit
PDB 1xrs EBI.jpg
crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and 5'-deoxyadenosine
Identifiers
Symbol Lys-AminoMut_A
Pfam PF09043
InterPro IPR015130

In enzymology, a D-lysine 5,6-aminomutase (EC 5.4.3.4) is an enzyme that catalyzes the chemical reaction

D-lysine \rightleftharpoons 2,5-diaminohexanoate

Hence, this enzyme has one substrate, D-lysine, and one product, 2,5-diaminohexanoate.

This enzyme belongs to the family of isomerases, specifically those intramolecular transferases transferring amino groups. The systematic name of this enzyme class is D-2,6-diaminohexanoate 5,6-aminomutase. Other names in common use include D-alpha-lysine mutase, and adenosylcobalamin-dependent D-lysine 5,6-aminomutase. This enzyme participates in lysine degradation. It employs one cofactor, cobamide.

Structure[edit]

The structure of the alpha subunit is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state.[1]

References[edit]

  1. ^ Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL (2004). "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase.". Proc Natl Acad Sci U S A 101 (45): 15870–5. doi:10.1073/pnas.0407074101. PMC 528771. PMID 15514022. 

Further reading[edit]

  • Morley CG, Stadtman TC (1970). "Studies on the fermentation of D-alpha-lysine. Purification and properties of an adenosine triphosphate regulated B 12-coenzyme-dependent D-alpha-lysine mutase complex from Clostridium sticklandii". Biochemistry. 9 (25): 4890–900. doi:10.1021/bi00827a010. PMID 5480154. 
  • Stadtman TC, Tsai L (1967). "A cobamide coenzyme dependent migration of the epsilon-amino group of D-lysine". Biochem. Biophys. Res. Commun. 28 (6): 920–6. doi:10.1016/0006-291X(67)90067-8. PMID 4229021. 

This article incorporates text from the public domain Pfam and InterPro IPR015130

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.

D-Lysine 5,6-aminomutase alpha subunit Provide feedback

Members of his family are involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state [1].

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015130

This domain is found in proteins involved in the 1,2 rearrangement of the terminal amino group of DL-lysine and of L-beta-lysine, using adenosylcobalamin (AdoCbl) and pyridoxal-5'-phosphate as cofactors. The structure is predominantly a PLP-binding TIM barrel domain, with several additional alpha-helices and beta-strands at the N and C termini. These helices and strands form an intertwined accessory clamp structure that wraps around the sides of the TIM barrel and extends up toward the Ado ligand of the Cbl cofactor, providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilising AdoCbl in the precatalytic resting state.

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 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
(8)
Full
(226)
Representative proteomes NCBI
(150)
Meta
(6)
RP15
(31)
RP35
(42)
RP55
(52)
RP75
(54)
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  Seed
(8)
Full
(226)
Representative proteomes NCBI
(150)
Meta
(6)
RP15
(31)
RP35
(42)
RP55
(52)
RP75
(54)
Alignment:
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Sequence:
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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
(8)
Full
(226)
Representative proteomes NCBI
(150)
Meta
(6)
RP15
(31)
RP35
(42)
RP55
(52)
RP75
(54)
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: pdb_1xrs
Previous IDs: none
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 8
Number in full: 226
Average length of the domain: 435.60 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 68.49 %

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 25.0 25.0
Trusted cut-off 70.2 70.1
Noise cut-off 17.5 17.3
Model length: 509
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

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

B12-binding Lys-AminoMut_A

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 Lys-AminoMut_A domain has been found. There are 25 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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