KAMD_ACESD
ID KAMD_ACESD Reviewed; 519 AA.
AC E3PRJ5; Q9ZFE6;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 11-JAN-2011, sequence version 1.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=Lysine 5,6-aminomutase alpha subunit {ECO:0000305};
DE Short=5,6-LAM {ECO:0000303|PubMed:11318641, ECO:0000303|PubMed:15514022};
DE EC=5.4.3.3 {ECO:0000269|PubMed:10617592, ECO:0000269|PubMed:11318641};
DE AltName: Full=D-lysine 5,6-aminomutase alpha subunit {ECO:0000312|EMBL:CBH21499.1};
DE AltName: Full=L-beta-lysine 5,6-aminomutase alpha subunit {ECO:0000305};
GN Name=kamD; OrderedLocusNames=CLOST_1379;
OS Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG
OS 9281 / NCIMB 10654 / HF) (Clostridium sticklandii).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Acetoanaerobium.
OX NCBI_TaxID=499177;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS,
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ACTIVITY REGULATION,
RP BIOPHYSICOCHEMICAL PROPERTIES, EPR SPECTROSCOPY, AND PATHWAY.
RX PubMed=10617592; DOI=10.1074/jbc.275.1.106;
RA Chang C.H., Frey P.A.;
RT "Cloning, sequencing, heterologous expression, purification, and
RT characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase
RT from Clostridium sticklandii.";
RL J. Biol. Chem. 275:106-114(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF;
RX PubMed=20937090; DOI=10.1186/1471-2164-11-555;
RA Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R.,
RA Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M.,
RA Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.;
RT "Clostridium sticklandii, a specialist in amino acid degradation:revisiting
RT its metabolism through its genome sequence.";
RL BMC Genomics 11:555-555(2010).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND REACTION MECHANISM.
RX PubMed=11318641; DOI=10.1021/bi010157j;
RA Tang K.H., Chang C.H., Frey P.A.;
RT "Electron transfer in the substrate-dependent suicide inactivation of
RT lysine 5,6-aminomutase.";
RL Biochemistry 40:5190-5199(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH B12 AND PYRIDOXAL
RP PHOSPHATE, COFACTOR, AND SUBUNIT.
RX PubMed=15514022; DOI=10.1073/pnas.0407074101;
RA Berkovitch F., Behshad E., Tang K.H., Enns E.A., Frey P.A., Drennan C.L.;
RT "A locking mechanism preventing radical damage in the absence of substrate,
RT as revealed by the x-ray structure of lysine 5,6-aminomutase.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:15870-15875(2004).
CC -!- FUNCTION: Catalyzes the migration of the L-beta-lysine and D-lysine
CC epsilon amino group to the delta carbon to produce 3,5-diaminohexanoate
CC and 2,5-diaminohexanoate, respectively. {ECO:0000269|PubMed:10617592,
CC ECO:0000269|PubMed:11318641}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate;
CC Xref=Rhea:RHEA:21736, ChEBI:CHEBI:57434, ChEBI:CHEBI:57436;
CC EC=5.4.3.3; Evidence={ECO:0000269|PubMed:11318641};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-lysine = (2R,5S)-2,5-diaminohexanoate; Xref=Rhea:RHEA:18241,
CC ChEBI:CHEBI:32557, ChEBI:CHEBI:137487; EC=5.4.3.3;
CC Evidence={ECO:0000269|PubMed:10617592, ECO:0000269|PubMed:11318641};
CC -!- COFACTOR:
CC Name=adenosylcob(III)alamin; Xref=ChEBI:CHEBI:18408;
CC Evidence={ECO:0000269|PubMed:10617592, ECO:0000269|PubMed:11318641};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000269|PubMed:11318641, ECO:0000269|PubMed:15514022};
CC -!- ACTIVITY REGULATION: Rapidly inactivated in the presence of D-lysine
CC and to a lesser extent in the absence of adenosylcobalamin (Adocbl).
CC Activity is stable in the presence of Adocbl when D-lysine is absent.
CC Adocbl imparts thermal stability at 37 degrees Celsius.
CC {ECO:0000269|PubMed:10617592}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=6.6 uM for adenosylcobalamin (for recombinant alpha and beta
CC subunits expressed together in E.coli to overcome the presence of
CC corrinoids in native system) {ECO:0000269|PubMed:10617592};
CC -!- PATHWAY: Amino-acid metabolism; lysine degradation.
CC {ECO:0000269|PubMed:10617592}.
CC -!- SUBUNIT: Heterotetramer of 2 alpha and 2 beta subunits.
CC {ECO:0000269|PubMed:15514022}.
CC -!- SIMILARITY: Belongs to the KamD family. {ECO:0000255}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CBH21499.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AF104259; AAC79717.1; -; Genomic_DNA.
DR EMBL; FP565809; CBH21499.1; ALT_INIT; Genomic_DNA.
DR PDB; 1XRS; X-ray; 2.80 A; A=5-519.
DR PDBsum; 1XRS; -.
DR AlphaFoldDB; E3PRJ5; -.
DR SMR; E3PRJ5; -.
DR IntAct; E3PRJ5; 1.
DR STRING; 1511.CLOST_1379; -.
DR PRIDE; E3PRJ5; -.
DR EnsemblBacteria; CBH21499; CBH21499; CLOST_1379.
DR KEGG; cst:CLOST_1379; -.
DR eggNOG; COG0274; Bacteria.
DR HOGENOM; CLU_517447_0_0_9; -.
DR OMA; SGLCMPE; -.
DR BRENDA; 5.4.3.3; 1522.
DR SABIO-RK; E3PRJ5; -.
DR UniPathway; UPA00225; -.
DR Proteomes; UP000007041; Chromosome.
DR GO; GO:0047702; F:beta-lysine 5,6-aminomutase activity; IEA:UniProtKB-EC.
DR GO; GO:0031419; F:cobalamin binding; IEA:UniProtKB-KW.
DR GO; GO:0047826; F:D-lysine 5,6-aminomutase activity; IEA:RHEA.
DR Gene3D; 3.20.20.440; -; 1.
DR InterPro; IPR016176; Cbl-dep_enz_cat.
DR InterPro; IPR015130; Lys-AminoMut_A.
DR InterPro; IPR037086; Lys-AminoMut_asu_sf.
DR Pfam; PF09043; Lys-AminoMut_A; 1.
DR SUPFAM; SSF51703; SSF51703; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalamin; Cobalt; Direct protein sequencing; Isomerase;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..519
FT /note="Lysine 5,6-aminomutase alpha subunit"
FT /id="PRO_0000416982"
FT BINDING 57..59
FT /ligand="adenosylcob(III)alamin"
FT /ligand_id="ChEBI:CHEBI:18408"
FT /evidence="ECO:0000269|PubMed:15514022"
FT BINDING 187..192
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:15514022"
FT BINDING 241
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:15514022"
FT BINDING 266
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:15514022"
FT BINDING 271
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:15514022"
FT BINDING 302
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000269|PubMed:15514022"
FT CONFLICT 4
FT /note="V -> M (in Ref. 1; AAC79717)"
FT /evidence="ECO:0000305"
FT HELIX 12..34
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 36..38
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 39..48
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 61..71
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 75..77
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 79..88
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 108..110
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 116..148
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 155..160
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 165..177
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 181..185
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 191..193
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 213..230
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 235..239
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 245..255
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 258..261
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 266..271
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 275..291
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 301..304
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 305..307
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 313..329
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 334..336
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 352..366
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 373..375
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 385..402
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 405..408
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 412..416
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 421..437
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 438..440
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 441..444
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 452..481
FT /evidence="ECO:0007829|PDB:1XRS"
FT TURN 482..487
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 498..500
FT /evidence="ECO:0007829|PDB:1XRS"
FT STRAND 501..503
FT /evidence="ECO:0007829|PDB:1XRS"
FT HELIX 511..516
FT /evidence="ECO:0007829|PDB:1XRS"
SQ SEQUENCE 519 AA; 57626 MW; 6FE0DEB4EC481DB1 CRC64;
MISVESKLNL DFNLVEKARA KAKAIAIDTQ EFIEKHTTVT VERAVCRLLG IDGVDTDEVP
LPNIVVDHIK ENNGLNLGAA MYIANAVLNT GKTPQEIAQA ISAGELDLTK LPMKDLFEVK
TKALSMAKET VEKIKNNRSI RESRFEEYGD KSGPLLYVIV ATGNIYEDIT QAVAAAKQGA
DVIAVIRTTG QSLLDYVPYG ATTEGFGGTY ATQENFRLMR EALDKVGAEV GKYIRLCNYC
SGLCMPEIAA MGAIERLDVM LNDALYGILF RDINMQRTMI DQNFSRIING FAGVIINTGE
DNYLTTADAF EEAHTVLASQ FINEQFALLA GLPEEQMGLG HAFEMDPELK NGFLYELSQA
QMAREIFPKA PLKYMPPTKF MTGNIFKGHI QDALFNMVTI MTNQRIHLLG MLTEALHTPF
MSDRALSIEN AQYIFNNMES ISEEIQFKED GLIQKRAGFV LEKANELLEE IEQLGLFDTL
EKGIFGGVKR PKDGGKGLNG VVSKDENYYN PFVELMLNK
