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O26158 (DAPAT_METTH) Reviewed, UniProtKB/Swiss-Prot

Last modified November 16, 2011. Version 76. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
LL-diaminopimelate aminotransferase
Short name=DAP-AT
Short name=DAP-aminotransferase
Short name=LL-DAP-aminotransferase
EC=2.6.1.83
Gene names
Name:dapL
Ordered Locus Names:MTH_52
OrganismMethanobacterium thermoautotrophicum (strain Delta H)
Taxonomic identifier187420 [NCBI]
Taxonomic lineageArchaea › Euryarchaeota › Methanobacteria › Methanobacteriales › Methanobacteriaceae › Methanothermobacter

Protein attributes

Sequence length410 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the synthesis of meso-diaminopimelate (m-DAP or DL-DAP), required for both lysine and peptidoglycan biosynthesis. Catalyzes the direct conversion of tetrahydrodipicolinate to LL-diaminopimelate, a reaction that requires three enzymes in E.coli. Is also able to catalyze the reverse reaction in vitro, i.e. the transamination of LL-diaminopimelate with 2-oxoglutarate to produce 2-oxo-6-aminopimelate (in equilibrium with tetrahydrodipicolinate) and glutamate. Has maximal aminotransferase activity using 2-oxoglutarate as an amino group acceptor, and can not use oxaloacetate instead of 2-oxoglutarate, although 2-oxoadipate can substitute with 21% relative activity. Can not use m-DAP, lysine or ornithine as the amino-group donor, when using 2-oxoglutarate as the amino-group acceptor. Ref.2 Ref.3

Catalytic activity

LL-2,6-diaminoheptanedioate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + L-glutamate + H2O. Ref.2

Cofactor

Pyridoxal phosphate. Ref.2

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; LL-2,6-diaminopimelate from (S)-tetrahydrodipicolinate (aminotransferase route): step 1/1. Ref.2 Ref.3

Subunit structure

Homodimer By similarity. HAMAP MF_01642

Sequence similarities

Belongs to the class-I pyridoxal-phosphate-dependent aminotransferase family. LL-diaminopimelate aminotransferase subfamily.

Biophysicochemical properties

Kinetic parameters:

KM=82 µM for LL-2,6-diaminopimelate Ref.3

KM=7.8 µM for L-2,3,4,5-tetrahydrodipicolinate

KM=2.6 mM for 2-oxoglutarate

KM=1.1 mM for glutamate

Vmax=6.3 µmol/min/mg enzyme for the forward reaction (tetrahydrodipicolinate synthesis)

Vmax=0.100 µmol/min/mg enzyme for the reverse reaction (LL-DAP synthesis)

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 410410LL-diaminopimelate aminotransferase HAMAP MF_01642
PRO_0000342256

Sites

Binding site421Substrate; via amide nitrogen By similarity
Binding site721Pyridoxal phosphate; shared with dimeric partner By similarity
Binding site751Substrate; shared with dimeric partner By similarity
Binding site1091Substrate By similarity
Binding site1321Substrate By similarity
Binding site1871Pyridoxal phosphate By similarity
Binding site1871Substrate By similarity
Binding site2151Pyridoxal phosphate By similarity
Binding site2181Pyridoxal phosphate By similarity
Binding site2461Pyridoxal phosphate By similarity
Binding site2481Pyridoxal phosphate By similarity
Binding site2571Pyridoxal phosphate By similarity
Binding site2921Substrate; shared with dimeric partner By similarity
Binding site3881Substrate By similarity

Amino acid modifications

Modified residue2491N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence LengthMass (Da)Tools
O26158 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: A9B03194E73DED5B

FASTA41046,213
        10         20         30         40         50         60 
MVTVNENYLL LKSSYIFSEI NRRVEEFQRK NPDADIIRMG IGDVTRPLPE AVVEAFHRAV 

        70         80         90        100        110        120 
DEMAEEETFR GYGPEQGYPF LREAIAENDY ASRGVDITAD EIFISDGAKC DTGNIQEIFG 

       130        140        150        160        170        180 
LDNVVAVTDP VYPVYVESNV MAGRAGPADD DGRYSGLVYL PCTEENSFIP SLPEERVDLI 

       190        200        210        220        230        240 
YLCYPNNPTG TTLTEKQLAE WVDYARDSGS LILFDAAYEA YIQEDGIPHS IYEVEGAREV 

       250        260        270        280        290        300 
AIEFRSFSKN AGFTGTRCAF TVVPEELEVP DSSGRMHSVR ELWNRRQTTK FNGVSYPVQR 

       310        320        330        340        350        360 
AAEAVYTPEG QREIRESIDY YMENARIIRE SLERAGLRYY GGVNAPYIWI RTPEGMDSWQ 

       370        380        390        400        410 
FFDTLLNDAE VVGTPGSGFG PSGEGYFRLT AFNSFRNTVK AMERISELSF

« Hide

References

« Hide 'large scale' references
[1]"Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics."
Smith D.R., Doucette-Stamm L.A., Deloughery C., Lee H.-M., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K., Harrison D., Hoang L., Keagle P., Lumm W., Pothier B., Qiu D., Spadafora R., Vicare R. expand/collapse author list , Wang Y., Wierzbowski J., Gibson R., Jiwani N., Caruso A., Bush D., Safer H., Patwell D., Prabhakar S., McDougall S., Shimer G., Goyal A., Pietrovski S., Church G.M., Daniels C.J., Mao J.-I., Rice P., Noelling J., Reeve J.N.
J. Bacteriol. 179:7135-7155(1997) [PubMed: 9371463] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: Delta H.
[2]"Methanogens with pseudomurein use diaminopimelate aminotransferase in lysine biosynthesis."
Graham D.E., Huse H.K.
FEBS Lett. 582:1369-1374(2008) [PubMed: 18371309] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, COFACTOR, PATHWAY.
Strain: Delta H.
[3]"Biochemical and phylogenetic characterization of a novel diaminopimelate biosynthesis pathway in prokaryotes identifies a diverged form of LL-diaminopimelate aminotransferase."
Hudson A.O., Gilvarg C., Leustek T.
J. Bacteriol. 190:3256-3263(2008) [PubMed: 18310350] [Abstract]
Cited for: FUNCTION, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, PATHWAY.
Strain: Delta H.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		AE000666 Genomic DNA. Translation: AAB84559.1.
PIRE69168.
RefSeqNP_275195.1. NC_000916.1.

3D structure databases

ProteinModelPortalO26158.
ModBaseSearch...

Protein-protein interaction databases

STRINGO26158.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID1470014.
GenomeReviewsGene locus MTH_52 in contig AE000666_GR.
KEGGmth:MTH52.
NMPDRfig|187420.1.peg.50.

Phylogenomic databases

eggNOGarNOG05001.
HOGENOMHBG645860.
OMARCAFTVV.
ProtClustDBPRK07590.

Enzyme and pathway databases

BioCycMTHE187420:MTH52-MONOMER.

Family and domain databases

HAMAPMF_01642. DapL_aminotrans_1.
[Tree]
InterProIPR004839. Aminotransferase_I/II.
IPR019942. DAP_NH2Trfase_plant/Chlamydia.
IPR015424. PyrdxlP-dep_Trfase_major_dom.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR015422. PyrdxlP-dep_Trfase_major_sub2.
[Graphical view]
Gene3DG3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.
G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.
KOK10206.
PANTHERPTHR11751:SF22. PTHR11751:SF22. 1 hit.
PfamPF00155. Aminotran_1_2. 1 hit.
[Graphical view]
SUPFAMSSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
TIGRFAMsTIGR03542. DAPAT_plant. 1 hit.
PROSITEPS00105. AA_TRANSFER_CLASS_1. False negative.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDAPAT_METTH
AccessionPrimary (citable) accession number: O26158
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 2008
Last sequence update: January 1, 1998
Last modified: November 16, 2011
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents