Q9Y948 (DEOC_AERPE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Deoxyribose-phosphate aldolase
Short name=DERA
EC=4.1.2.4

Alternative name(s):
2-deoxy-D-ribose 5-phosphate aldolase
Phosphodeoxyriboaldolase
Short name=Deoxyriboaldolase

Gene names

Name:	deoC
Ordered Locus Names:	APE_2437.1

Organism

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) [Complete proteome] [HAMAP]

Taxonomic identifier

272557 [NCBI]

Taxonomic lineage

Archaea › Crenarchaeota › Thermoprotei › Desulfurococcales › Desulfurococcaceae › Aeropyrum

Protein attributes

Sequence length	235 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate. Ref.2
Catalytic activity	2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde. Ref.2
Pathway	Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate: step 2/2. HAMAP MF_00114
Subunit structure	Homotetramer. Ref.2
Subcellular location	Cytoplasm By similarity HAMAP MF_00114.
Biotechnological use	Its high stability makes the enzyme a potential candidate to be used as a synthetic catalyst in practical application. Ref.2
Miscellaneous	The enzyme is also highly resistant to organic solvents such as ethanol, methanol, N,N-dimethylformamide, and Me2SO at 50 degrees Celsius. Loss of activity is not observed in the presence of these reagents even at a concentration as high as 40%. HAMAP MF_00114
Sequence similarities	Belongs to the DeoC/FbaB aldolase family. DeoC type 1 subfamily.
Biophysicochemical properties	Kinetic parameters: KM=0.057 mM for 2-deoxy-D-ribose 5-phosphate Ref.2 pH dependence: Optimum pH is 6.5. Is extremely stable over a wide pH range: upon heating at 50 degrees Celsius for 60 minutes, the enzyme does not lose activity at pH 4.5-11.0. Temperature dependence: Extremely thermostable. Retains full activity upon heating at 100 degrees Celsius for 10 minutes and at 80 degrees Celsius for 60 minutes.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Schiff base
Molecular function	Lyase
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	carbohydrate metabolic process Inferred from direct assay Ref.2. Source: UniProtKB deoxyribonucleotide catabolic process Inferred from electronic annotation. Source: InterPro protein tetramerization Inferred from direct assay Ref.2. Source: UniProtKB
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	deoxyribose-phosphate aldolase activity Inferred from direct assay Ref.2. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2

Chain

2 – 235

234

Deoxyribose-phosphate aldolase HAMAP MF_00114

PRO_0000057286

Sites

Active site

167

1

Schiff-base intermediate with acetaldehyde By similarity

Active site

197

1

By similarity

Secondary structure

1

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235

Helix Strand Turn

Details...

Helix

4 – 14

11

Helix

18 – 22

5

Beta strand

25 – 28

4

Helix

36 – 49

14

Beta strand

54 – 56

3

Helix

58 – 71

14

Beta strand

75 – 80

6

Turn

81 – 83

3

Helix

88 – 101

14

Beta strand

105 – 108

4

Helix

112 – 114

3

Helix

116 – 132

17

Beta strand

136 – 140

5

Helix

143 – 145

3

Helix

148 – 160

13

Beta strand

164 – 168

5

Beta strand

171 – 173

3

Helix

179 – 189

11

Helix

190 – 192

3

Beta strand

195 – 201

7

Helix

205 – 213

9

Beta strand

217 – 221

5

Helix

224 – 232

9

Sequences

	Sequence		Length	Mass (Da)
	Q9Y948 [UniParc]. Last modified November 1, 2002. Version 2. Checksum: 64CE582A38DCFD38	FASTA	235	24,529
	10 20 30 40 50 60 MPSARDILQQ GLDRLGSPED LASRIDSTLL SPRATEEDVR NLVREASDYG FRCAVLTPVY 70 80 90 100 110 120 TVKISGLAEK LGVKLCSVIG FPLGQAPLEV KLVEAQTVLE AGATELDVVP HLSLGPEAVY 130 140 150 160 170 180 REVSGIVKLA KSYGAVVKVI LEAPLWDDKT LSLLVDSSRR AGADIVKTST GVYTKGGDPV 190 200 210 220 230 TVFRLASLAK PLGMGVKASG GIRSGIDAVL AVGAGADIIG TSSAVKVLES FKSLV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1." Kawarabayasi Y., Hino Y., Horikawa H., Yamazaki S., Haikawa Y., Jin-no K., Takahashi M., Sekine M., Baba S., Ankai A., Kosugi H., Hosoyama A., Fukui S., Nagai Y., Nishijima K., Nakazawa H., Takamiya M., Masuda S. , Funahashi T., Tanaka T., Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Kubota K., Nakamura Y., Nomura N., Sako Y., Kikuchi H. DNA Res. 6:83-101(1999) [PubMed: 10382966] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.
[2]	"The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-D-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix." Sakuraba H., Tsuge H., Shimoya I., Kawakami R., Goda S., Kawarabayasi Y., Katunuma N., Ago H., Miyano M., Ohshima T. J. Biol. Chem. 278:10799-10806(2003) [PubMed: 12529358] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), PROTEIN SEQUENCE OF 2-13, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, BIOTECHNOLOGY. Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

BA000002 Genomic DNA. Translation: BAA81452.2.

PIR

D72474.

RefSeq

NP_148609.2. NC_000854.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1N7K	X-ray	2.00	A/B	2-235	[»]

ProteinModelPortal

Q9Y948.

SMR

Q9Y948. Positions 2-235.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

GeneID

1445418.

GenomeReviews

Gene locus APE_2437.1 in contig BA000002_GR.

KEGG

ape:APE_2437.1.

NMPDR

fig|272557.1.peg.1717.

Organism-specific databases

CMR

Search...

Phylogenomic databases

HOGENOM

HBG636421.

OMA

IAIVNES.

PhylomeDB

Q9Y948.

Enzyme and pathway databases

BioCyc

APER272557:APE2437-MONOMER.

Family and domain databases

HAMAP

MF_00114. DeoC_type1.
[Tree]

InterPro

IPR013785. Aldolase_TIM.
IPR011343. DeoC.
IPR002915. DeoC/AroFGH_arch.
IPR022979. Deoxyribose_phosphate_aldo_1.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.

KO

K01619.

PANTHER

PTHR10889. DeoC. 1 hit.

Pfam

PF01791. DeoC. 1 hit.
[Graphical view]

PIRSF

PIRSF001357. DeoC. 1 hit.

TIGRFAMs

TIGR00126. DeoC. 1 hit.

ProtoNet

Search...

Entry information

Entry name

DEOC_AERPE

Accession

Primary (citable) accession number: Q9Y948

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	November 1, 2002
Last modified:	December 14, 2011
This is version 80 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program