Skip Header

Contribute Send feedback
Read comments (?) or add your own

Q0IBD1 (Q0IBD1_SYNS3) Unreviewed, UniProtKB/TrEMBL

Last modified May 1, 2013. Version 50. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein namesRecommended name:
Diaminopimelate decarboxylase HAMAP-Rule MF_02120
Short name=DAP decarboxylase HAMAP-Rule MF_02120
Short name=DAPDC HAMAP-Rule MF_02120
EC=4.1.1.20 HAMAP-Rule MF_02120
Gene names
Name:lysA HAMAP-Rule MF_02120
Ordered Locus Names:sync_1029
OrganismSynechococcus sp. (strain CC9311) [Complete proteome] [HAMAP] EMBL ABI46923.1
Taxonomic identifier64471 [NCBI]
Taxonomic lineageBacteria › Cyanobacteria › Oscillatoriophycideae › Chroococcales › Synechococcus

Protein attributes

Sequence length453 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine By similarity. HAMAP-Rule MF_02120

Catalytic activity

Meso-2,6-diaminoheptanedioate = L-lysine + CO2. HAMAP-Rule MF_02120 RuleBase RU003738

Cofactor

Pyridoxal phosphate By similarity. HAMAP-Rule MF_02120 RuleBase RU003738 SAAS SAAS022644

Pathway

Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; L-lysine from DL-2,6-diaminopimelate: step 1/1. HAMAP-Rule MF_02120 RuleBase RU003738

Subunit structure

Homodimer By similarity. HAMAP-Rule MF_02120

Sequence similarities

Belongs to the Orn/Lys/Arg decarboxylase class-II family. LysA subfamily. HAMAP-Rule MF_02120

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

Region303 – 3064Pyridoxal phosphate binding By similarity HAMAP-Rule MF_02120

Sites

Binding site2611Pyridoxal phosphate; via amide nitrogen By similarity HAMAP-Rule MF_02120
Binding site3061Substrate By similarity HAMAP-Rule MF_02120
Binding site3431Substrate By similarity HAMAP-Rule MF_02120
Binding site3471Substrate By similarity HAMAP-Rule MF_02120
Binding site3751Substrate By similarity HAMAP-Rule MF_02120
Binding site4031Pyridoxal phosphate By similarity HAMAP-Rule MF_02120
Binding site4031Substrate By similarity HAMAP-Rule MF_02120

Amino acid modifications

Modified residue831N6-(pyridoxal phosphate)lysine By similarity HAMAP-Rule MF_02120

Sequences

Sequence LengthMass (Da)Tools
Q0IBD1 [UniParc].

Last modified October 3, 2006. Version 1.
Checksum: 6BECB0319AAD8BF4

FASTA45348,909
        10         20         30         40         50         60 
MATPYESGCD HVSPNRNLAP VSAELDDLGR LMVGGCRLSE LAERYGTPLY VLDEVTIRAS 

        70         80         90        100        110        120 
AQEYREALKR HYPGDSLAVY ASKAHSSLAL TGLVASEGLG LDAVSAGELL TALDGGMPPE 

       130        140        150        160        170        180 
RMVLHGNNKS VEELALAYSH GVMVVADNQH DLDCLAELVP QGGGPVRLML RFTPGIECHT 

       190        200        210        220        230        240 
HEYIRTGHLD SKFGFDPDQL QPVLTALAGC AWARVEGLHA HIGSQIFELD PHRDLAAVMA 

       250        260        270        280        290        300 
DALKLARELG HPVRDLNVGG GLGIRYVESD DPPSIDAWVK VVAEAVTLAC RERGLELPRL 

       310        320        330        340        350        360 
MCEPGRSLVA SSGVTVYTVG ARKVVPGIRT YVSVDGGMSD NPRPITYQSL YTACLADRPL 

       370        380        390        400        410        420 
AQADETITLA GKHCESGDVL LKDLSFPSCR SGEVLVVLAT GAYNLSMSSN YNRIPRPAAV 

       430        440        450 
LVNQGEAELI QRREQPEDLL RYDLMPDRLR SVK

« Hide

References

[1]"Genome sequence of Synechococcus CC9311: insights into adaptation to a coastal environment."
Palenik B., Ren Q., Dupont C.L., Myers G.S., Heidelberg J.F., Badger J.H., Madupu R., Nelson W.C., Brinkac L.M., Dodson R.J., Durkin A.S., Daugherty S.C., Sullivan S.A., Khouri H., Mohamoud Y., Halpin R., Paulsen I.T.
Proc. Natl. Acad. Sci. U.S.A. 103:13555-13559(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CC9311.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		CP000435 Genomic DNA. Translation: ABI46923.1.
RefSeqYP_730241.1. NC_008319.1.

3D structure databases

ProteinModelPortalQ0IBD1.
ModBaseSearch...

Protein-protein interaction databases

STRING64471.sync_1029.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaABI46923; ABI46923; sync_1029.
GeneID4258875.
KEGGsyg:sync_1029.
PATRIC23793036. VBISynSp88089_1081.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0019.
HOGENOMHOG000045071.
KOK01586.
OMAQGIDCHI.
ProtClustDBCLSK826046.

Enzyme and pathway databases

UniPathwayUPA00034; UER00027.

Family and domain databases

Gene3D2.40.37.10. 1 hit.
HAMAPMF_02120. LysA.
InterProIPR009006. Ala_racemase/Decarboxylase_C.
IPR002986. DAP_deCOOHase_LysA.
IPR022643. De-COase2_C.
IPR022657. De-COase2_CS.
IPR022644. De-COase2_N.
IPR022653. De-COase2_pyr-phos_BS.
IPR000183. Orn/DAP/Arg_de-COase.
[Graphical view]
PfamPF02784. Orn_Arg_deC_N. 1 hit.
PF00278. Orn_DAP_Arg_deC. 1 hit.
[Graphical view]
PRINTSPR01181. DAPDCRBXLASE.
PR01179. ODADCRBXLASE.
SUPFAMSSF50621. Racem_decarbox_C. 1 hit.
TIGRFAMsTIGR01048. lysA. 1 hit.
PROSITEPS00878. ODR_DC_2_1. 1 hit.
PS00879. ODR_DC_2_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameQ0IBD1_SYNS3
AccessionPrimary (citable) accession number: Q0IBD1
Entry history
Integrated into UniProtKB/TrEMBL: October 3, 2006
Last sequence update: October 3, 2006
Last modified: May 1, 2013
This is version 50 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info