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25  structures 425  species 0  interactions 562  sequences 3  architectures

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

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

# D-lysine 5,6-aminomutase

D-Lysine 5,6-aminomutase alpha subunit
crystal structure of lysine 5,6-aminomutase in complex with plp, cobalamin, and 5'-deoxyadenosine
Identifiers
SymbolLys-AminoMut_A
PfamPF09043
InterProIPR015130
D-lysine 5,6-aminomutase
Identifiers
EC number5.4.3.4
CAS number9075-70-1
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structures
Gene Ontology

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

D-lysine ${\displaystyle \rightleftharpoons }$ 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.

## 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-Î±-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 Îµ-carbon to Î´-carbon in both D-lysine and L-Î²-lysine, and catalyzing the migration of hydrogen atoms from Î´-carbon to Îµ-carbon at the same time.[1] It demonstrates greatest catalytic activity in 20mM Trisâ€¢HCl at pH 9.0-9.2.[2]

In the early 1950s, 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-Î±-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-Î²-lysine to 3,5-diaminohexanoic acid.[3][4]

## Structure

### Subunits

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

5,6-LAM is an Î±2Î²2 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 Î² subunit binds AdoCbl while the PLP directly binds to Î± subunit. PLP also directly binds to Lys144 of the Î² subunit to form an internal aldimine. PLP and AdoCbl are separated by a distance of 24Ã….[6]

### Cofactors

1. 5,6-LAM is pyridoxal-5'-phosphate (PLP) dependent. 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]
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

### 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 Ã…. PLP participates in multiple non-covalent interactions with the enzyme with 5,6-LAM presenting an â€œopenâ€ state.

The first step of the catalytic cycle involves the enzyme accepting the substrate by forming an external aldimine with PLP replacing the PLP-Lys144Î² internal aldimine. With the cleavage of the internal aldimine, the Î² unit is able to swing towards to the top of the Î± unit and block the empty site. Therefore, generation of the Ado-CH2â€¢ 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 â€œclosedâ€ 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 Î² 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 Tyr263Î± is oriented in a slipped geometry with pyridine ring of PLP, generating a Ï€-Ï€ 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 Î±-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 Iâ€¢. Based on quantum-mechanical calculations, it was proposed that with 5-fluorolysine[9] as a substitute for D-lysine the 5-FSâ€¢ species can be captured and analyzed. A similar approach was applied towards PLP modification, when it was modified to 4â€™-cyanoPLP[13] or PLP-NO.[14] The radical intermediate Iâ€¢ 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): 16004â€“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): 4890â€“900. doi:10.1021/bi00827a010. 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): 651â€“7. PMC 357300. 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): 920â€“6. doi:10.1016/0006-291x(67)90067-8. 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): 15870â€“5. doi:10.1073/pnas.0407074101. PMC 528771. 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): 6399â€“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-263Î± as revealed by electron paramagnetic resonance spectroscopy". Journal of the American Chemical Society. 133 (43): 17152â€“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): 2325â€“9. doi:10.1021/bi00788a023. 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: 1â€“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): 788â€“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): 15870â€“5. doi:10.1073/pnas.0407074101. PMC 528771. 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): 8678â€“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): 161â€“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-5â€²-phosphate-N-oxide with Lysine 5,6-Aminomutase: Enzyme Flexibility toward Cofactor Analog". ACS Catalysis. 5 (5): 3093â€“3099. doi:10.1021/acscatal.5b00671.
This article incorporates text from the public domain Pfam and InterPro: IPR015130

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

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

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...

# Pfam Clan

This family is a member of clan TIM_barrel (CL0036), which has the following description:

This large superfamily of TIM barrel enzymes all contain a common phosphate binding site. The phosphate is found in a variety of cofactors and ligands such as FMN [1,2].

The clan contains the following 61 members:

Lys-AminoMut_A

# 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 and the UniProtKB 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
(30)
Full
(562)
Representative proteomes UniProt
(1866)
RP15
(99)
RP35
(335)
RP55
(582)
RP75
(842)
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PP/heatmap 1 View

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

Key: available, not generated, not available.

## Format an alignment

Seed
(30)
Full
(562)
Representative proteomes UniProt
(1866)
RP15
(99)
RP35
(335)
RP55
(582)
RP75
(842)
Alignment:
Format:
Order:
Sequence:
Gaps:

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
(30)
Full
(562)
Representative proteomes UniProt
(1866)
RP15
(99)
RP35
(335)
RP55
(582)
RP75
(842)

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.

# 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

 Seed source: pdb_1xrs Previous IDs: none Type: Domain Sequence Ontology: SO:0000417 Author: Mistry J , Sammut SJ Number in seed: 30 Number in full: 562 Average length of the domain: 475.40 aa Average identity of full alignment: 48 % Average coverage of the sequence by the domain: 83.11 %

## HMM information

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 27.8 27.4
Noise cut-off 24.8 24.6
Model length: 508
Family (HMM) version: 13

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