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E3PRJ4

- KAMED_CLOSD

UniProt

E3PRJ4 - KAMED_CLOSD

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Protein

D-lysine 5,6-aminomutase beta subunit

Gene

kamE

Organism
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Status
Reviewed - 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 presence of corrinoids in native system)1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi133 – 1331Cobalt (adenosylcobalamin axial ligand); via tele nitrogenImported

GO - Molecular functioni

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

Keywords - Molecular functioni

Isomerase

Keywords - Ligandi

Cobalamin, Cobalt, Metal-binding, Pyridoxal phosphate

Enzyme and pathway databases

BioCyciCSTI499177:GJE9-1427-MONOMER.
UniPathwayiUPA00225.

Names & Taxonomyi

Protein namesi
Recommended name:
D-lysine 5,6-aminomutase beta subunitImported (EC:5.4.3.41 Publication)
Short name:
5,6-LAM1 Publication
Gene namesi
Name:kamE
Ordered Locus Names:CLOST_1378
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 – 262262D-lysine 5,6-aminomutase beta subunitPRO_0000416984Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei144 – 1441N6-(pyridoxal phosphate)lysine1 Publication

Interactioni

Subunit structurei

Heterotetramer of 2 alpha and 2 beta subunits.1 Publication

Protein-protein interaction databases

IntActiE3PRJ4. 1 interaction.

Structurei

Secondary structure

1
262
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi34 – 429Combined sources
Helixi46 – 5712Combined sources
Beta strandi65 – 739Combined sources
Beta strandi76 – 838Combined sources
Helixi106 – 11611Combined sources
Beta strandi121 – 1288Combined sources
Helixi135 – 1417Combined sources
Helixi152 – 1543Combined sources
Beta strandi158 – 1625Combined sources
Beta strandi165 – 1673Combined sources
Helixi169 – 17810Combined sources
Beta strandi182 – 1876Combined sources
Helixi195 – 20915Combined sources
Helixi213 – 2153Combined sources
Beta strandi216 – 2216Combined sources
Helixi227 – 2315Combined sources
Turni232 – 2343Combined sources
Beta strandi236 – 2394Combined sources
Helixi245 – 26016Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XRSX-ray2.80B1-262[»]
ProteinModelPortaliE3PRJ4.
SMRiE3PRJ4. Positions 33-261.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini120 – 262143B12-bindingPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni130 – 1367Adenosylcobalamin binding1 Publication
Regioni185 – 1928Adenosylcobalamin binding1 Publication
Regioni219 – 2235Adenosylcobalamin binding1 Publication
Regioni239 – 2446Adenosylcobalamin binding1 Publication

Sequence similaritiesi

Belongs to the KamE family.Sequence Analysis
Contains 1 B12-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

HOGENOMiHOG000223896.
KOiK18011.
OMAiPYGDRRD.

Family and domain databases

Gene3Di3.30.30.60. 1 hit.
3.40.50.280. 1 hit.
InterProiIPR006158. Cobalamin-bd.
IPR028991. KamE_N.
[Graphical view]
PfamiPF02310. B12-binding. 1 hit.
[Graphical view]
SUPFAMiSSF117778. SSF117778. 1 hit.
SSF52242. SSF52242. 1 hit.
PROSITEiPS51332. B12_BINDING. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

E3PRJ4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSSGLYSMEK KEFDKVLDLE RVKPYGDTMN DGKVQLSFTL PLKNNERSAE
60 70 80 90 100
AAKQIALKMG LEEPSVVMQQ SLDEEFTFFV VYGNFVQSVN YNEIHVEAVN
110 120 130 140 150
SEILSMEETD EYIKENIGRK IVVVGASTGT DAHTVGIDAI MNMKGYAGHY
160 170 180 190 200
GLERYEMIDA YNLGSQVANE DFIKKAVELE ADVLLVSQTV TQKNVHIQNM
210 220 230 240 250
THLIELLEAE GLRDRFVLLC GGPRINNEIA KELGYDAGFG PGRFADDVAT
260
FAVKTLNDRM NS
Length:262
Mass (Da):29,224
Last modified:March 8, 2011 - v1
Checksum:i248765160F6EF46F
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF104259 Genomic DNA. Translation: AAC79718.1.
FP565809 Genomic DNA. Translation: CBH21498.1.
RefSeqiYP_003936403.1. NC_014614.1.

Genome annotation databases

EnsemblBacteriaiCBH21498; CBH21498; CLOST_1378.
GeneIDi9854875.
KEGGicst:CLOST_1378.
PATRICi42273391. VBICloSti32817_1367.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF104259 Genomic DNA. Translation: AAC79718.1 .
FP565809 Genomic DNA. Translation: CBH21498.1 .
RefSeqi YP_003936403.1. NC_014614.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1XRS X-ray 2.80 B 1-262 [» ]
ProteinModelPortali E3PRJ4.
SMRi E3PRJ4. Positions 33-261.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi E3PRJ4. 1 interaction.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CBH21498 ; CBH21498 ; CLOST_1378 .
GeneIDi 9854875.
KEGGi cst:CLOST_1378.
PATRICi 42273391. VBICloSti32817_1367.

Phylogenomic databases

HOGENOMi HOG000223896.
KOi K18011.
OMAi PYGDRRD.

Enzyme and pathway databases

UniPathwayi UPA00225 .
BioCyci CSTI499177:GJE9-1427-MONOMER.

Family and domain databases

Gene3Di 3.30.30.60. 1 hit.
3.40.50.280. 1 hit.
InterProi IPR006158. Cobalamin-bd.
IPR028991. KamE_N.
[Graphical view ]
Pfami PF02310. B12-binding. 1 hit.
[Graphical view ]
SUPFAMi SSF117778. SSF117778. 1 hit.
SSF52242. SSF52242. 1 hit.
PROSITEi PS51332. B12_BINDING. 1 hit.
[Graphical view ]
ProtoNeti Search...

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 nameiKAMED_CLOSD
AccessioniPrimary (citable) accession number: E3PRJ4
Secondary accession number(s): Q9ZFE5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 18, 2012
Last sequence update: March 8, 2011
Last modified: November 26, 2014
This is version 25 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