L-lysine 2,3-aminomutase - Clostridium subterminale

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Q9XBQ8 (KAMA_CLOSU) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 60. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
L-lysine 2,3-aminomutase
Short name=LAM
EC=5.4.3.2

Alternative name(s):
KAM

Gene names

Name:

kamA

Organism

Clostridium subterminale

Taxonomic identifier

1550 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	416 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the interconversion of L-alpha-lysine and L-beta-lysine. Ref.2 Ref.4 Ref.5
Catalytic activity	L-lysine = (3S)-3,6-diaminohexanoate. Ref.2
Cofactor	Binds 1 4Fe-4S cluster per subunit. The cluster is coordinated with 3 cysteines and an exchangeable S-adenosyl-L-methionine. Ref.2 Ref.4 Ref.5 Ref.8 Pyridoxal phosphate. Ref.2 Ref.4 Ref.5 Ref.8 Binds 1 Co²⁺ ion per subunit. Ref.2 Ref.4 Ref.5 Ref.8 Binds 1 zinc ion per subunit. Ref.2 Ref.4 Ref.5 Ref.8
Enzyme regulation	The enzyme is activated by S-adenosyl-methionine. Activity is dependent on the levels of Fe²⁺, S²- and Co²⁺. Activity is stimulated by addition of EDTA. S-adenosylhomocysteine competitively inhibits the activity whereas 5'-methylthioadenosine is not inhibitory in the presence of S-adenosylmethionine. Competitively inhibited by 4-thialysine. Inhibited by sodium borohydride (1 mM) when added with 2 mM dithionate. Moderately inhibited by beta-mercaptoethanol (30 mM) along with dithionate. Higher concentrations of Fe²⁺ partially inhibit the activity and Co²⁺ at 1 mM is a strong inhibitor. Hydroxylamine, isonicotinic acid hydrazide inhibit effectively, in addition, hydrazine, D-penicillamine and D-cycloserine are also inhibitory at high concentrations. Ref.2 Ref.4 Ref.6
Pathway	Amino-acid degradation; L-lysine degradation via acetate pathway.
Subunit structure	Homohexamer; trimer of dimers. Forms a homotetramer in crystal. Ref.3
Sequence similarities	Belongs to the radical SAM superfamily. KamA family.
Biophysicochemical properties	Kinetic parameters: K_M=6.6 µM for L-lysine Ref.2 Ref.5 Ref.6 K_M=28 nM for adenosylmethionine K_M=1.4 mM for 4-thialysine V_max=0.19 µmol/min/mg enzyme with 4-thialysine as substrate (at 37 degrees Celsius and pH 8) pH dependence: Optimum pH is 8.0. Displays half maximal activity between pH 6.0 and 9.8. Redox potential: E₀ is between -336 and -370 mV for 4Fe-4S cluster. Temperature dependence: Optimum temperature is 37 degrees Celsius. It has strong activity at 37 degrees Celsius but is reversibly inactivated in temperatures between 37 and 65 degrees Celsius. Minimal loss of activity is observed in enzyme stored at -10 degrees Celsius in the presence of 15% glycerol.

Ontologies

Keywords
Ligand	4Fe-4S Cobalt Iron Iron-sulfur Metal-binding Pyridoxal phosphate S-adenosyl-L-methionine Zinc
Molecular function	Isomerase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	L-lysine catabolic process to acetate Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	4 iron, 4 sulfur cluster binding Inferred from electronic annotation. Source: UniProtKB-KW lysine 2,3-aminomutase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 416

416

L-lysine 2,3-aminomutase

PRO_0000172287

Sites

Metal binding

125

Iron-sulfur (4Fe-4S-S-AdoMet)

Metal binding

129

Iron-sulfur (4Fe-4S-S-AdoMet)

Metal binding

132

Iron-sulfur (4Fe-4S-S-AdoMet)

Metal binding

268

Zinc

Metal binding

375

Zinc

Metal binding

377

Zinc

Metal binding

380

Zinc

Amino acid modifications

Modified residue

337

N6-(pyridoxal phosphate)lysine

Experimental info

Mutagenesis

E → Q: Reduction in activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

D → N: Reduction in activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

130

R → Q or K: Complete loss of activity. Decrease in iron and sulfide but not PLP content. Destabilise the iron-sulfur centers. Ref.7

Mutagenesis

134

R → K: Complete loss of activity. Significant decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

134

R → Q: Complete loss of activity. Slight decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

135

R → K: Reduction in activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

135

R → Q: Reduction in activity. Significant decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

136

R → Q: Reduction in activity. Significant decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

165

D → N: Significant reduction in activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

172

D → N: Complete loss of activity. Decrease in iron and sulfide and PLP content. Destabilise the iron-sulfur centers. Ref.7

Mutagenesis

236

E → Q: Significant reduction in activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

293

D → N: Complete loss of activity. Decrease in iron and sulfide and PLP content. Ref.7

Mutagenesis

330

D → A or N: Complete loss of activity. Decrease in iron and sulfide and PLP content. Ref.7

Secondary structure

416

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Q9XBQ8 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: 6C3602E5B87E25A1
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FASTA

416

47,102

        10         20         30         40         50         60 
MINRRYELFK DVSDADWNDW RWQVRNRIET VEELKKYIPL TKEEEEGVAQ CVKSLRMAIT 

        70         80         90        100        110        120 
PYYLSLIDPN DPNDPVRKQA IPTALELNKA AADLEDPLHE DTDSPVPGLT HRYPDRVLLL 

       130        140        150        160        170        180 
ITDMCSMYCR HCTRRRFAGQ SDDSMPMERI DKAIDYIRNT PQVRDVLLSG GDALLVSDET 

       190        200        210        220        230        240 
LEYIIAKLRE IPHVEIVRIG SRTPVVLPQR ITPELVNMLK KYHPVWLNTH FNHPNEITEE 

       250        260        270        280        290        300 
STRACQLLAD AGVPLGNQSV LLRGVNDCVH VMKELVNKLV KIRVRPYYIY QCDLSLGLEH 

       310        320        330        340        350        360 
FRTPVSKGIE IIEGLRGHTS GYCVPTFVVD APGGGGKTPV MPNYVISQSH DKVILRNFEG 

       370        380        390        400        410 
VITTYSEPIN YTPGCNCDVC TGKKKVHKVG VAGLLNGEGM ALEPVGLERN KRHVQE

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References

[1]	"Lysine 2,3-aminomutase from Clostridium subterminale SB4: mass spectral characterization of cyanogen bromide-treated peptides and cloning, sequencing, and expression of the gene kamA in Escherichia coli." Ruzicka F.J., Lieder K.W., Frey P.A. J. Bacteriol. 182:469-476(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-16; 342-389 AND 401-416, CHARACTERIZATION. Strain: SB4.
[2]	"Lysine 2,3-aminomutase. Purification and properties of a pyridoxal phosphate and S-adenosylmethionine-activated enzyme." Chirpich T.P., Zappia V., Costilow R.N., Barker H.A. J. Biol. Chem. 245:1778-1789(1970) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION.
[3]	"Molecular properties of lysine-2,3-aminomutase." Song K.B., Frey P.A. J. Biol. Chem. 266:7651-7655(1991) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT. Strain: SB4.
[4]	"Metal cofactors of lysine-2,3-aminomutase." Petrovich R.M., Ruzicka F.J., Reed G.H., Frey P.A. J. Biol. Chem. 266:7656-7660(1991) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, COFACTOR, ENZYME REGULATION.
[5]	"Characterization of iron-sulfur clusters in lysine 2,3-aminomutase by electron paramagnetic resonance spectroscopy." Petrovich R.M., Ruzicka F.J., Reed G.H., Frey P.A. Biochemistry 31:10774-10781(1992) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
[6]	"Inhibition of lysine 2,3-aminomutase by the alternative substrate 4-thialysine and characterization of the 4-thialysyl radical intermediate." Miller J., Bandarian V., Reed G.H., Frey P.A. Arch. Biochem. Biophys. 387:281-288(2001) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.
[7]	"Identification of structural and catalytic classes of highly conserved amino acid residues in lysine 2,3-aminomutase." Chen D., Frey P.A., Lepore B.W., Ringe D., Ruzicka F.J. Biochemistry 45:12647-12653(2006) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF GLU-86; ASP-96; ARG-130; ARG-134; ARG-135; ARG-136; ASP-165; ASP-172; GLU-236; ASP-293 AND ASP-330.
[8]	"The X-ray crystal structure of lysine-2,3-aminomutase from Clostridium subterminale." Lepore B.W., Ruzicka F.J., Frey P.A., Ringe D. Proc. Natl. Acad. Sci. U.S.A. 102:13819-13824(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE AND COFACTORS. Strain: SB4.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF159146 Genomic DNA. Translation: AAD43134.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2A5H	X-ray	2.10	A/B/C/D	1-416	[»]

ProteinModelPortal

Q9XBQ8.

SMR

Q9XBQ8. Positions 3-412.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-12270.

UniPathway

UPA00870.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR025895. LAM_C_dom.
IPR022459. Lysine_aminomutase.
IPR003739. Lysine_aminomutase_fam.
IPR007197. rSAM.
[Graphical view]

Pfam

PF12544. LAM_C. 1 hit.
PF04055. Radical_SAM. 1 hit.
[Graphical view]

PIRSF

PIRSF004911. DUF160. 1 hit.

TIGRFAMs

TIGR03820. lys_2_3_AblA. 1 hit.
TIGR00238. TIGR00238. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q9XBQ8.

Entry information

Entry name

KAMA_CLOSU

Accession

Primary (citable) accession number: Q9XBQ8

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 24, 2006
Last sequence update:	November 1, 1999
Last modified:	May 29, 2013
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Sites

Amino acid modifications

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Enzyme and pathway databases

Family and domain databases

Other

Entry information

Relevant documents