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E3PRJ5

- KAMDD_CLOSD

UniProt

E3PRJ5 - KAMDD_CLOSD

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Protein

D-lysine 5,6-aminomutase alpha subunit

Gene
kamD, CLOST_1379
Organism
Clostridium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654)
Status
Reviewed - Annotation score: 5 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

Adenosylcobalamin.2 Publications
Pyridoxal phosphate.2 Publications

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 subunit (EC:5.4.3.4)
Short name:
5,6-LAM
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 – 3423
Beta strandi36 – 383
Helixi39 – 4810
Helixi61 – 7111
Turni75 – 773
Helixi79 – 8810
Helixi94 – 10310
Turni108 – 1103
Helixi116 – 14833
Beta strandi155 – 1606
Helixi165 – 17713
Beta strandi181 – 1855
Helixi191 – 1933
Helixi213 – 23018
Beta strandi235 – 2395
Helixi245 – 25511
Beta strandi258 – 2614
Helixi266 – 2716
Helixi275 – 29117
Beta strandi295 – 2973
Helixi301 – 3044
Beta strandi305 – 3073
Turni309 – 3113
Helixi313 – 32917
Helixi334 – 3363
Beta strandi340 – 3423
Helixi352 – 36615
Beta strandi373 – 3753
Helixi385 – 40218
Beta strandi405 – 4084
Turni412 – 4165
Helixi421 – 43717
Turni438 – 4403
Helixi441 – 4444
Helixi452 – 48130
Turni482 – 4876
Helixi498 – 5003
Beta strandi501 – 5033
Helixi511 – 5166

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1XRSX-ray2.80A5-519[»]

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.

Phylogenomic databases

HOGENOMiHOG000223893.
KOiK01844.
OMAiFRDINMK.

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

MISVESKLNL DFNLVEKARA KAKAIAIDTQ EFIEKHTTVT VERAVCRLLG    50
IDGVDTDEVP LPNIVVDHIK ENNGLNLGAA MYIANAVLNT GKTPQEIAQA 100
ISAGELDLTK LPMKDLFEVK TKALSMAKET VEKIKNNRSI RESRFEEYGD 150
KSGPLLYVIV ATGNIYEDIT QAVAAAKQGA DVIAVIRTTG QSLLDYVPYG 200
ATTEGFGGTY ATQENFRLMR EALDKVGAEV GKYIRLCNYC SGLCMPEIAA 250
MGAIERLDVM LNDALYGILF RDINMQRTMI DQNFSRIING FAGVIINTGE 300
DNYLTTADAF EEAHTVLASQ FINEQFALLA GLPEEQMGLG HAFEMDPELK 350
NGFLYELSQA QMAREIFPKA PLKYMPPTKF MTGNIFKGHI QDALFNMVTI 400
MTNQRIHLLG MLTEALHTPF MSDRALSIEN AQYIFNNMES ISEEIQFKED 450
GLIQKRAGFV LEKANELLEE IEQLGLFDTL EKGIFGGVKR PKDGGKGLNG 500
VVSKDENYYN PFVELMLNK 519
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.

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti4 – 41V → M in AAC79717. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
Links Updated
AF104259 Genomic DNA. Translation: AAC79717.1 .
FP565809 Genomic DNA. Translation: CBH21499.1 . Different initiation.
RefSeqi YP_003936404.1. NC_014614.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1XRS X-ray 2.80 A 5-519 [» ]
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

IntActi E3PRJ5. 1 interaction.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai CBH21499 ; CBH21499 ; CLOST_1379 .
GeneIDi 9856102.
KEGGi cst:CLOST_1379.
PATRICi 42273393. VBICloSti32817_1368.

Phylogenomic databases

HOGENOMi HOG000223893.
KOi K01844.
OMAi FRDINMK.

Enzyme and pathway databases

UniPathwayi UPA00225 .
BioCyci CSTI499177:GJE9-1428-MONOMER.

Family and domain databases

Gene3Di 3.20.20.440. 1 hit.
InterProi IPR016176. Cbl-dep_enz_cat.
IPR015130. Lys-AminoMut_A.
[Graphical view ]
Pfami PF09043. Lys-AminoMut_A. 1 hit.
[Graphical view ]
SUPFAMi SSF51703. SSF51703. 1 hit.
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 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: September 3, 2014
This is version 18 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

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

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