C6E9Q9 (DAPA_GEOSM) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
4-hydroxy-tetrahydrodipicolinate synthase
Short name=HTPA synthase
EC=4.3.3.7

Gene names

Name:	dapA
Ordered Locus Names:	GM21_4144

Organism

Geobacter sp. (strain M21) [Complete proteome] [HAMAP]

Taxonomic identifier

443144 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › delta/epsilon subdivisions › Deltaproteobacteria › Desulfuromonadales › Geobacteraceae › Geobacter

Protein attributes

Sequence length	290 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA) By similarity. HAMAP-Rule MF_00418
Catalytic activity	Pyruvate + L-aspartate-4-semialdehyde = (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate + H2O. HAMAP-Rule MF_00418
Pathway	Amino-acid biosynthesis; L-lysine biosynthesis via DAP pathway; (S)-tetrahydrodipicolinate from L-aspartate: step 3/4. HAMAP-Rule MF_00418
Subunit structure	Homotetramer; dimer of dimers By similarity.
Subcellular location	Cytoplasm By similarity.
Sequence similarities	Belongs to the DapA family.
Caution	Was originally thought to be a dihydrodipicolinate synthase (DHDPS), catalyzing the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to dihydrodipicolinate (DHDP). However, it was shown in E.coli (PubMed:8993314 and PubMed:20503968) that the product of the enzymatic reaction is not dihydrodipicolinate but in fact (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid (HTPA), and that the consecutive dehydration reaction leading to DHDP is not spontaneous but catalyzed by DapB (PubMed:20503968).

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Diaminopimelate biosynthesis Lysine biosynthesis
Cellular component	Cytoplasm
Ligand	Schiff base
Molecular function	Lyase
Technical term	Complete proteome
Gene Ontology (GO)
Biological_process	diaminopimelate biosynthetic process Inferred from electronic annotation. Source: HAMAP lysine biosynthetic process via diaminopimelate Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	4-hydroxy-tetrahydrodipicolinate synthase Inferred from electronic annotation. Source: EC amine-lyase activity Inferred from electronic annotation. Source: HAMAP
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 290	290	4-hydroxy-tetrahydrodipicolinate synthase HAMAP-Rule MF_00418		PRO_1000206032
Sites
	Active site	132	1	Proton donor/acceptor By similarity
	Active site	160	1	Schiff-base intermediate with substrate By similarity
	Binding site	44	1	Pyruvate By similarity
	Binding site	202	1	Pyruvate; via carbonyl oxygen By similarity
	Site	43	1	Part of a proton relay during catalysis By similarity
	Site	106	1	Part of a proton relay during catalysis By similarity

Sequences

	Sequence		Length	Mass (Da)
	C6E9Q9 [UniParc]. Last modified September 1, 2009. Version 1. Checksum: DAE5F200048602D7	FASTA	290	31,103
	10 20 30 40 50 60 MFQGSIVAIV TPFKNGAVDE EKLRELVEFQ IENGTDAIVP CGTTGESSTL SYVEHDRVIQ 70 80 90 100 110 120 VVVEQVNKRV PVIAGTGSNS THEAIEITQH AKELGADGAL LVTPYYNKPS QEGLFRHYKA 130 140 150 160 170 180 VADAVALPQI LYNVPGRTGV NLLPETVARL SVHQNIVAIK EATGSLQQAS EVLALCGDKI 190 200 210 220 230 240 DVLSGDDFIT LPIMAAGGKG VISVTANIMP KEVSSLVDAF NAGNLEEARR LHLYLLKISN 250 260 270 280 290 AMFIESNPVP VKAAVSLMGK CSSEVRLPLA PLMEANLAKL TAIMKEYKLI

References

[1]

"Complete sequence of Geobacter sp. M21." US DOE Joint Genome Institute Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H., Bruce D., Goodwin L., Pitluck S., Saunders E., Brettin T., Detter J.C., Han C., Larimer F., Land M., Hauser L., Kyrpides N., Ovchinnikova G., Lovley D. Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: M21.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CP001661 Genomic DNA. Translation: ACT20159.1.
RefSeq	YP_003023917.1. NC_012918.1.
3D structure databases
ProteinModelPortal	C6E9Q9.
ModBase	Search...
Protein-protein interaction databases
STRING	443144.GM21_4144.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	ACT20159; ACT20159; GM21_4144.
GeneID	8139518.
KEGG	gem:GM21_4144.
PATRIC	22022718. VBIGeoSp56140_4049.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0329.
HOGENOM	HOG000173604.
KO	K01714.
OMA	VNALFSV.
ProtClustDB	PRK03170.
Enzyme and pathway databases
BioCyc	GSP443144:GHKM-4219-MONOMER.
UniPathway	UPA00034; UER00017.
Family and domain databases
Gene3D	3.20.20.70. 1 hit.
HAMAP	MF_00418. DapA.
InterPro	IPR013785. Aldolase_TIM. IPR002220. Dihydrodipicolinate_synth-like. IPR020625. Dihydrodipicolinate_synth_AS. IPR020624. Dihydrodipicolinate_synth_CS. IPR005263. Dihydrodipicolinate_synth_DapA. [Graphical view]
PANTHER	PTHR12128. PTHR12128. 1 hit.
Pfam	PF00701. DHDPS. 1 hit. [Graphical view]
PIRSF	PIRSF001365. DHDPS. 1 hit.
PRINTS	PR00146. DHPICSNTHASE.
TIGRFAMs	TIGR00674. dapA. 1 hit.
PROSITE	PS00665. DHDPS_1. 1 hit. PS00666. DHDPS_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DAPA_GEOSM

Accession

Primary (citable) accession number: C6E9Q9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 22, 2009
Last sequence update:	September 1, 2009
Last modified:	May 1, 2013
This is version 30 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program