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Protein

D-lysine 5,6-aminomutase alpha subunit

Gene

kamD

Organism
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the 1,2-migration of the D-lysine epsilon amino group to the delta carbon with concomitant reverse migration of a hydrogen atom to produce 2,5-diaminohexanoic acid.1 Publication

Catalytic activityi

D-lysine = 2,5-diaminohexanoate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • adenosylcob(III)alamin1 Publication
  • pyridoxal 5'-phosphate1 Publication

Enzyme regulationi

Rapidly inactivated in the presence of D-lysine and to a lesser extent in the absence of adenosylcobalamin (Adocbl). Activity is stable in the presence of Adocbl when D-lysine is absent. Adocbl imparts thermal stability at 37 degrees Celsius.1 Publication

Kineticsi

  1. KM=6.6 µM for adenosylcobalamin (for recombinant alpha and beta subunits expressed together in E.coli to overcome the presence of corrinoids in native system)1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei238 – 2381Pyridoxal phosphate1 Publication
Binding sitei263 – 2631Pyridoxal phosphate1 Publication
Binding sitei268 – 2681Pyridoxal phosphate1 Publication
Binding sitei299 – 2991Pyridoxal phosphate1 Publication

GO - Molecular functioni

  1. cobalamin binding Source: UniProtKB-KW
  2. D-lysine 5,6-aminomutase activity Source: UniProtKB-EC
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Cobalamin, Cobalt, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciCSTI499177:GJE9-1428-MONOMER.
UniPathwayiUPA00225.

Names & Taxonomyi

Protein namesi
Recommended name:
D-lysine 5,6-aminomutase alpha subunitImported (EC:5.4.3.41 Publication)
Short name:
5,6-LAM1 Publication
Gene namesi
Name:kamD
Ordered Locus Names:CLOST_1379
OrganismiClostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Taxonomic identifieri499177 [NCBI]
Taxonomic lineageiBacteriaFirmicutesClostridiaClostridialesPeptostreptococcaceaePeptoclostridium
ProteomesiUP000007041: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 519519D-lysine 5,6-aminomutase alpha subunitPRO_0000416982Add
BLAST

Interactioni

Subunit structurei

Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

Protein-protein interaction databases

IntActiE3PRJ5. 1 interaction.

Structurei

Secondary structure

1
519
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi12 – 3423Combined sources
Beta strandi36 – 383Combined sources
Helixi39 – 4810Combined sources
Helixi61 – 7111Combined sources
Turni75 – 773Combined sources
Helixi79 – 8810Combined sources
Helixi94 – 10310Combined sources
Turni108 – 1103Combined sources
Helixi116 – 14833Combined sources
Beta strandi155 – 1606Combined sources
Helixi165 – 17713Combined sources
Beta strandi181 – 1855Combined sources
Helixi191 – 1933Combined sources
Helixi213 – 23018Combined sources
Beta strandi235 – 2395Combined sources
Helixi245 – 25511Combined sources
Beta strandi258 – 2614Combined sources
Helixi266 – 2716Combined sources
Helixi275 – 29117Combined sources
Beta strandi295 – 2973Combined sources
Helixi301 – 3044Combined sources
Beta strandi305 – 3073Combined sources
Turni309 – 3113Combined sources
Helixi313 – 32917Combined sources
Helixi334 – 3363Combined sources
Beta strandi340 – 3423Combined sources
Helixi352 – 36615Combined sources
Beta strandi373 – 3753Combined sources
Helixi385 – 40218Combined sources
Beta strandi405 – 4084Combined sources
Turni412 – 4165Combined sources
Helixi421 – 43717Combined sources
Turni438 – 4403Combined sources
Helixi441 – 4444Combined sources
Helixi452 – 48130Combined sources
Turni482 – 4876Combined sources
Helixi498 – 5003Combined sources
Beta strandi501 – 5033Combined sources
Helixi511 – 5166Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XRSX-ray2.80A5-519[»]
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni54 – 563Adenosylcobalamin binding1 Publication
Regioni184 – 1896Pyridoxal phosphate binding1 Publication

Sequence similaritiesi

Belongs to the KamD family.Sequence Analysis

Phylogenomic databases

HOGENOMiHOG000223893.
KOiK01844.
OMAiATQENFR.

Family and domain databases

Gene3Di3.20.20.440. 1 hit.
InterProiIPR016176. Cbl-dep_enz_cat.
IPR015130. Lys-AminoMut_A.
[Graphical view]
PfamiPF09043. Lys-AminoMut_A. 1 hit.
[Graphical view]
SUPFAMiSSF51703. SSF51703. 1 hit.

Sequencei

Sequence statusi: Complete.

E3PRJ5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MISVESKLNL DFNLVEKARA KAKAIAIDTQ EFIEKHTTVT VERAVCRLLG
60 70 80 90 100
IDGVDTDEVP LPNIVVDHIK ENNGLNLGAA MYIANAVLNT GKTPQEIAQA
110 120 130 140 150
ISAGELDLTK LPMKDLFEVK TKALSMAKET VEKIKNNRSI RESRFEEYGD
160 170 180 190 200
KSGPLLYVIV ATGNIYEDIT QAVAAAKQGA DVIAVIRTTG QSLLDYVPYG
210 220 230 240 250
ATTEGFGGTY ATQENFRLMR EALDKVGAEV GKYIRLCNYC SGLCMPEIAA
260 270 280 290 300
MGAIERLDVM LNDALYGILF RDINMQRTMI DQNFSRIING FAGVIINTGE
310 320 330 340 350
DNYLTTADAF EEAHTVLASQ FINEQFALLA GLPEEQMGLG HAFEMDPELK
360 370 380 390 400
NGFLYELSQA QMAREIFPKA PLKYMPPTKF MTGNIFKGHI QDALFNMVTI
410 420 430 440 450
MTNQRIHLLG MLTEALHTPF MSDRALSIEN AQYIFNNMES ISEEIQFKED
460 470 480 490 500
GLIQKRAGFV LEKANELLEE IEQLGLFDTL EKGIFGGVKR PKDGGKGLNG
510
VVSKDENYYN PFVELMLNK
Length:519
Mass (Da):57,626
Last modified:January 11, 2011 - v1
Checksum:i6FE0DEB4EC481DB1
GO

Sequence cautioni

The sequence CBH21499.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41V → M in AAC79717. (PubMed:10617592)Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF104259 Genomic DNA. Translation: AAC79717.1.
FP565809 Genomic DNA. Translation: CBH21499.1. Different initiation.
RefSeqiYP_003936404.1. NC_014614.1.

Genome annotation databases

EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379.
GeneIDi9856102.
KEGGicst:CLOST_1379.
PATRICi42273393. VBICloSti32817_1368.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF104259 Genomic DNA. Translation: AAC79717.1.
FP565809 Genomic DNA. Translation: CBH21499.1. Different initiation.
RefSeqiYP_003936404.1. NC_014614.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XRSX-ray2.80A5-519[»]
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiE3PRJ5. 1 interaction.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCBH21499; CBH21499; CLOST_1379.
GeneIDi9856102.
KEGGicst:CLOST_1379.
PATRICi42273393. VBICloSti32817_1368.

Phylogenomic databases

HOGENOMiHOG000223893.
KOiK01844.
OMAiATQENFR.

Enzyme and pathway databases

UniPathwayiUPA00225.
BioCyciCSTI499177:GJE9-1428-MONOMER.

Family and domain databases

Gene3Di3.20.20.440. 1 hit.
InterProiIPR016176. Cbl-dep_enz_cat.
IPR015130. Lys-AminoMut_A.
[Graphical view]
PfamiPF09043. Lys-AminoMut_A. 1 hit.
[Graphical view]
SUPFAMiSSF51703. SSF51703. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequencing, heterologous expression, purification, and characterization of adenosylcobalamin-dependent D-lysine 5, 6-aminomutase from Clostridium sticklandii."
    Chang C.H., Frey P.A.
    J. Biol. Chem. 275:106-114(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF N-TERMINUS, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, EPR SPECTROSCOPY, PATHWAY.
  2. "Clostridium sticklandii, a specialist in amino acid degradation:revisiting its metabolism through its genome sequence."
    Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R., Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M., Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.
    BMC Genomics 11:555-555(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654.
  3. "A locking mechanism preventing radical damage in the absence of substrate, as revealed by the x-ray structure of lysine 5,6-aminomutase."
    Berkovitch F., Behshad E., Tang K.H., Enns E.A., Frey P.A., Drennan C.L.
    Proc. Natl. Acad. Sci. U.S.A. 101:15870-15875(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH B12 AND PYRIDOXAL PHOSPHATE, COFACTOR, SUBUNIT.

Entry informationi

Entry nameiKAMDD_CLOSD
AccessioniPrimary (citable) accession number: E3PRJ5
Secondary accession number(s): Q9ZFE6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2012
Last sequence update: January 11, 2011
Last modified: January 7, 2015
This is version 22 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.