Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
25  structures 199  species 3  interactions 245  sequences 3  architectures

Family: Lys-AminoMut_A (PF09043)

Summary: D-Lysine 5,6-aminomutase TIM-barrel domain of alpha subunit

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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 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
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

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

D-lysine 2,5-diaminohexanoate

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

This enzyme participates in lysine degradation. It employs one cofactor, cobamide.

Two pathways of lysine degradation

Background

D-lysine 5,6-aminomutase belongs to the isomerase family of enzymes, specifically intramolecular transferases, which transfers amino groups. Its systematic name is D-2,6-diaminohexanoate 5,6-aminomutase. Other names in common use include D-α-lysine mutase and adenosylcobalamin-dependent D-lysine 5,6-aminomutase, which can be abbreviated as 5,6-LAM.

Mutase reaction of 5,6-LAM

5,6-LAM is capable of reversibly catalyzing the migration of an amino group from ε-carbon to δ-carbon in both D-lysine and L-β-lysine, and catalyzing the migration of hydrogen atoms from δ-carbon to ε-carbon at the same time.[1] It demonstrates greatest catalytic activity in 20mM Tris•HCl at pH 9.0-9.2.[2]

In the early 1950's, 5,6-LAM was discovered in the amino-acid-fermenting bacteria Clostridium sticklandii, in which lysine undergoes degradation under anaerobic conditions to equimolar amounts of acetate and butyrate.[3]

Later, isotopic studies uncovered two possible pathways. In pathway A, both acetate and butyrate are generated from C2-C3 cleavage of D-lysine. Unlike pathway A, pathway B involves C5-C4 degradation, producing the same products.

D-lysine 5,6-aminomutase (5,6-LAM) is responsible for the first conversion in pathway B to convert D-α-lysine into 2,5-diaminohexanoate. Unlike other members of the family of aminomutases (like 2,3-LAM), which are peculiar to a single substrate, 5,6-LAM can reversibly catalyze both the reaction of D-lysine to 2,5-diaminohexanoic acid and the reaction of L-β-lysine to 3,5-diaminohexanoic acid.[3][4]

5,6-LAM Catalyzed Reactions of Lysin.jpeg

Structure

Subunits

Two units of 5,6-LAM (AdoCbl in yellow and PLP in orange)

5,6-LAM is an α2β2 tetramer. 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, which is the beta subunit providing most of the interactions observed between the protein and the Ado ligand of the Cbl, suggesting that its role is mainly in stabilizing AdoCbl in the precatalytic resting state.[5] The β subunit binds AdoCbl while the PLP directly binds to α subunit. PLP also directly binds to Lys144 of the β subunit to form an internal aldimine. PLP and AdoCbl are separated by a distance of 24Å.[6]

Cofactors

  1. 5,6-LAM is pyridoxal-5'-phosphate (PLP) dependant. PLP binds to its substrate with an external aldimine linkage. PLP is also important for stabilizing the radical intermediate by captodative stabilization and spin delocalization.[7]
  2. Catalysis begins with a 5'-deoxyadenosyl radical (Ado-CH2•), and 5'-deoxyadenosylcobalamin (AdoCbl) is an essential cofactor as a hydrogen carrier.[8]
  3. ATP, a mercaptan, and a divalent metal ion (usually Mg2+) are required to achieve the highest catalytic effect.[4]

Mechanism

Proposed Mechanism of 5,6-LAM

Catalytic cycle

The catalytic cycle starts with Ado-CH2• (5'-deoxyadenosyl radical derived from adenosylcobalamine) abstracting a hydrogen atom from PLP-D-lysine adduct (substrate-related precursor SH) to generate a substrate-related radical (S•), with the radical located at carbon 5 of the lysine residue. The latter undergoes an internal cyclization/addition to the imine nitrogen producing an aziridinecarbinyl radical (I•) — a more thermodynamically stable intermediate with the radical being at a benzylic position. Rearrangement of I• produces a product-related radical (P•), which then participates in the final step of hydrogen transfer from AdoH to afford the PLP-product complex (PH).[9]

Structure-based catalysis

Further understanding of the catalytic mechanism can be derived from the X-ray structure.

PLP (in green) maintains much interaction with enzyme in open state

First, an evident conformational change is observed after the substrate is added to the system. With a substrate-free enzyme, the distance between AdoCbl and PLP is about 24 Å. PLP participates in multiple non-covalent interactions with the enzyme with 5,6-LAM presenting an “open” state.

The first step of the catalytic cycle involves the enzyme accepting the substrate by forming an external aldimine with PLP replacing the PLP-Lys144β internal aldimine. With the cleavage of the internal aldimine, the β unit is able to swing towards to the top of the α unit and block the empty site. Therefore, generation of the Ado-CH2• radical leads to a change in the structure of the active domain, bringing the AdoCbl and PLP-substrate complex closer to each other, thus locking the enzyme in a “closed” state. The closed state exists until the radical transfer occurs when the product is released and AdoCbl is reformed. At the same time, the closed state is transformed to the open state again to wait for the next substrate.[10]

Also worth mentioning is the locking mechanism to prevent the radical reaction without the presence of substrate discovered by Catherine Drennan’s group. Lys144 of the β subunit is located at a short G-rich loop highly conserved across all 5,6-LAMs, which blocks the AdoCbl from the reaction site. Based on X-ray structure analysis, when the open structure is applied, the axes of the TIM barrel and Rossmann domains are in different directions. With the addition of the substrate, the subunits rearrange to turn the axes into each other to facilitate the catalysis.[11] For example, in wild type 5,6-LAM, the phenol ring of Tyr263α is oriented in a slipped geometry with pyridine ring of PLP, generating a π-π stacking interaction, which is capable of modulating the electron distribution of the high-energetic radical intermediate.[12]

History

Early insights into the mechanism of the catalytic reaction mainly focused on isotopic methods. Both pathways of lysine degradation and the role of 5,6-LAM were discovered in early work by Stadtman’s group during 1950s-1960s. In 1971, having a tritiated α-lysine, 2,5-diaminohexanoate, and coenzyme in hand, Colin Morley and T. Stadtman discovered the role of 5'-deoxyadenosylcobalamin (AdoCbl) as a source for hydrogen migration.[8] Recently, much progress has been made toward detecting the intermediates of the reaction, especially towards I•. Based on quantum-mechanical calculations, it was proposed that with 5-fluorolysine[9] as a substitute for D-lysine the 5-FS• species can be captured and analyzed. A similar approach was applied towards PLP modification, when it was modified to 4’-cyanoPLP[13] or PLP-NO.[14] The radical intermediate I• analogue is hypothesized to be easily detected to support the proposed mechanism. Other simulations can also provide some insights into the catalytic reaction.[1]

References

  1. ^ a b Sandala GM, Smith DM, Radom L (December 2006). "In search of radical intermediates in the reactions catalyzed by lysine 2,3-aminomutase and lysine 5,6-aminomutase". Journal of the American Chemical Society. 128 (50): 16004–5. doi:10.1021/ja0668421. PMID 17165731. 
  2. ^ Morley CG, Stadtman TC (December 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. PMID 5480154. 
  3. ^ a b Stadtman TC, White FH (June 1954). "Tracer studies on ornithine, lysine, and formate metabolism in an amino acid fermenting Clostridium". Journal of Bacteriology. 67 (6): 651–7. PMC 357300Freely accessible. PMID 13174491. 
  4. ^ a b Stadtman TC, Tsai L (September 1967). "A cobamide coenzyme dependent migration of the epsilon-amino group of D-lysine". Biochemical and Biophysical Research Communications. 28 (6): 920–6. PMID 4229021. 
  5. ^ Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL (November 2004). "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase". Proceedings of the National Academy of Sciences of the United States of America. 101 (45): 15870–5. doi:10.1073/pnas.0407074101. PMC 528771Freely accessible. PMID 15514022. 
  6. ^ Lo HH, Lin HH, Maity AN, Ke SC (May 2016). "The molecular mechanism of the open-closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase". Chemical Communications. 52 (38): 6399–402. doi:10.1039/c6cc01888b. PMID 27086547. 
  7. ^ Chen YH, Maity AN, Pan YC, Frey PA, Ke SC (November 2011). "Radical stabilization is crucial in the mechanism of action of lysine 5,6-aminomutase: role of tyrosine-263α as revealed by electron paramagnetic resonance spectroscopy". Journal of the American Chemical Society. 133 (43): 17152–5. doi:10.1021/ja207766c. PMID 21939264. 
  8. ^ a b Morley CG, Stadtman TC (June 1971). "Studies on the fermentation of p-alpha-lysine. On the hydrogen shift catalyzed by the B 12 coenzyme dependent D-alpha-lysine mutase". Biochemistry. 10 (12): 2325–9. PMID 5114991. 
  9. ^ a b Maity AN, Ke S (October 2013). "5-Fluorolysine as alternative substrate of lysine 5,6-aminomutase: A computational study". Computational and Theoretical Chemistry. 1022: 1–5. doi:10.1016/j.comptc.2013.08.007. 
  10. ^ Chen Y, Maity AN, Frey PA, Ke S (January 2013). "Mechanism-based Inhibition Reveals Transitions between Two Conformational States in the Action of Lysine 5,6-Aminomutase: A Combination of Electron Paramagnetic Resonance Spectroscopy, Electron Nuclear Double Resonance Spectroscopy, and Density Functional Theory Study". Journal of the American Chemical Society. 135 (2): 788–794. doi:10.1021/ja309603a. 
  11. ^ Berkovitch F, Behshad E, Tang KH, Enns EA, Frey PA, Drennan CL (November 2004). "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase". Proceedings of the National Academy of Sciences of the United States of America. 101 (45): 15870–5. doi:10.1073/pnas.0407074101. PMC 528771Freely accessible. PMID 15514022. 
  12. ^ Wetmore SD, Smith DM, Radom L (September 2001). "Enzyme catalysis of 1,2-amino shifts: the cooperative action of B6, B12, and aminomutases". Journal of the American Chemical Society. 123 (36): 8678–89. doi:10.1021/ja010211j. PMID 11535072. 
  13. ^ Maity AN, Ke SC (February 2015). "4'-CyanoPLP presents better prospect for the experimental detection of elusive cyclic intermediate radical in the reaction of lysine 5,6-aminomutase". Biochemical and Biophysical Research Communications. 457 (2): 161–4. doi:10.1016/j.bbrc.2014.12.076. PMID 25542154. 
  14. ^ Maity AN, Lin H, Chiang H, Lo H, Ke S (May 2015). "Reaction of Pyridoxal-5′-phosphate-N-oxide with Lysine 5,6-Aminomutase: Enzyme Flexibility toward Cofactor Analog". ACS Catalysis. 5 (5): 3093–3099. doi:10.1021/acscatal.5b00671. 

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 TIM-barrel domain of 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 co-factors. 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 co-factor, 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]. This is a TIM-barrel domain.

Literature references

  1. Wolthers KR, Levy C, Scrutton NS, Leys D;, J Biol Chem. 2010;285:13942-13950.: Large-scale domain dynamics and adenosylcobalamin reorientation orchestrate radical catalysis in ornithine 4,5-aminomutase. PUBMED:20106986 EPMC:20106986


Internal 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...

Loading domain graphics...

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...

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
(33)
Full
(245)
Representative proteomes UniProt
(537)
NCBI
(891)
Meta
(6)
RP15
(67)
RP35
(184)
RP55
(249)
RP75
(329)
Jalview View  View  View  View  View  View  View  View  View 
HTML View  View               
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
(33)
Full
(245)
Representative proteomes UniProt
(537)
NCBI
(891)
Meta
(6)
RP15
(67)
RP35
(184)
RP55
(249)
RP75
(329)
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
(33)
Full
(245)
Representative proteomes UniProt
(537)
NCBI
(891)
Meta
(6)
RP15
(67)
RP35
(184)
RP55
(249)
RP75
(329)
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: pdb_1xrs
Previous IDs: none
Type: Domain
Author: Mistry J, Sammut SJ
Number in seed: 33
Number in full: 245
Average length of the domain: 468.20 aa
Average identity of full alignment: 46 %
Average coverage of the sequence by the domain: 80.68 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.5 26.3
Noise cut-off 23.8 23.7
Model length: 508
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 3 interactions for this family. More...

B12-binding 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.

Loading structure mapping...