Q96AT9 (RPE_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribulose-phosphate 3-epimerase
EC=5.1.3.1

Alternative name(s):
Ribulose-5-phosphate-3-epimerase

Gene names

Name:	RPE
ORF Names:	HUSSY-17

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate. Ref.6
Catalytic activity	D-ribulose 5-phosphate = D-xylulose 5-phosphate. Ref.6
Cofactor	Binds 1 divalent metal cation per subunit. Contains tightly bound Fe2+ when produced in E.coli, but the physiological cofactor may be Co2+, Mn2+ or Zn2+. Ref.6
Subunit structure	Homodimer.
Sequence similarities	Belongs to the ribulose-phosphate 3-epimerase family.
Sequence caution	The sequence BAB71076.1 differs from that shown. Reason: Frameshift at position 69. The sequence BAC04212.1 differs from that shown. Reason: Frameshift at position 42.

Ontologies

Keywords
Biological process	Carbohydrate metabolism
Coding sequence diversity	Alternative splicing
Ligand	Cobalt Manganese Metal-binding Zinc
Molecular function	Isomerase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	pentose-phosphate shunt Inferred from direct assay Ref.6. Source: UniProtKB pentose-phosphate shunt, non-oxidative branch Inferred from electronic annotation. Source: Compara
Cellular_component	cytosol Traceable author statement. Source: Reactome intracellular membrane-bounded organelle Inferred from electronic annotation. Source: Compara
Molecular_function	metal ion binding Inferred from direct assay Ref.6. Source: UniProtKB monosaccharide binding Inferred from electronic annotation. Source: Compara ribulose-phosphate 3-epimerase activity Inferred from direct assay Ref.6. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
itself		2	EBI-372480,EBI-372480

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q96AT9-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q96AT9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     43-68: Missing.
     114-114: K → KSCSVTQAEVQWHSQGPLQ

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 228

228

Ribulose-phosphate 3-epimerase

PRO_0000171587

Regions

Region

146 – 149

4

Substrate binding

Region

197 – 198

2

Substrate binding

Sites

Active site

37

1

Proton acceptor Probable

Active site

175

1

Proton donor Probable

Metal binding

35

1

Divalent metal cation

Metal binding

37

1

Divalent metal cation

Metal binding

70

1

Divalent metal cation

Metal binding

175

1

Divalent metal cation

Binding site

10

1

Substrate

Binding site

70

1

Substrate

Binding site

177

1

Substrate; via amide nitrogen

Natural variations

Alternative sequence

43 – 68

26

Missing in isoform 2.

VSP_008317

Alternative sequence

114

1

K → KSCSVTQAEVQWHSQGPLQ in isoform 2.

VSP_008318

Experimental info

Mutagenesis

10

1

S → A: Nearly abolishes enzyme activity. Ref.6

Mutagenesis

12

1

L → A: Reduces enzyme activity by half. Ref.6

Mutagenesis

35

1

H → A: Alters protein structure. Nearly abolishes enzyme activity. Ref.6

Mutagenesis

37

1

D → A: Alters protein structure. Nearly abolishes enzyme activity. Ref.6

Mutagenesis

39

1

M → A: Lowers enzyme activity by 10%. Ref.6

Mutagenesis

70

1

H → A: Alters protein structure. Ref.6

Mutagenesis

72

1

M → A: Reduces enzyme activity by half. Ref.6

Mutagenesis

141

1

M → A: No effect on enzyme activity. Ref.6

Mutagenesis

175

1

D → A: Alters protein structure. Ref.6

Sequence conflict

180

1

P → L in BAC04212. Ref.1

Secondary structure

1

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228

Helix Strand Turn

Details...

Beta strand

6 – 10

5

Helix

16 – 18

3

Helix

19 – 28

10

Beta strand

34 – 45

12

Helix

51 – 61

11

Beta strand

63 – 65

3

Beta strand

67 – 72

6

Helix

76 – 79

4

Helix

80 – 86

7

Beta strand

89 – 94

6

Helix

95 – 97

3

Helix

101 – 110

10

Beta strand

114 – 119

6

Helix

125 – 127

3

Helix

129 – 134

6

Beta strand

136 – 143

8

Turn

145 – 147

3

Helix

154 – 156

3

Helix

157 – 166

10

Beta strand

171 – 177

7

Turn

180 – 182

3

Helix

183 – 189

7

Beta strand

193 – 197

5

Helix

198 – 201

4

Helix

206 – 223

18

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified December 1, 2001. Version 1. Checksum: 447130018AC52331	FASTA	228	24,928
	10 20 30 40 50 60 MASGCKIGPS ILNSDLANLG AECLRMLDSG ADYLHLDVMD GHFVPNITFG HPVVESLRKQ 70 80 90 100 110 120 LGQDPFFDMH MMVSKPEQWV KPMAVAGANQ YTFHLEATEN PGALIKDIRE NGMKVGLAIK 130 140 150 160 170 180 PGTSVEYLAP WANQIDMALV MTVEPGFGGQ KFMEDMMPKV HWLRTQFPSL DIEVDGGVGP 190 200 210 220 DTVHKCAEAG ANMIVSGSAI MRSEDPRSVI NLLRNVCSEA AQKRSLDR
	Isoform 2 [UniParc]. Checksum: 626FAFD9426AE406	FASTA	220	23,924
	10 20 30 40 50 60 MASGCKIGPS ILNSDLANLG AECLRMLDSG ADYLHLDVMD GHMHMMVSKP EQWVKPMAVA 70 80 90 100 110 120 GANQYTFHLE ATENPGALIK DIRENGMKSC SVTQAEVQWH SQGPLQVGLA IKPGTSVEYL 130 140 150 160 170 180 APWANQIDMA LVMTVEPGFG GQKFMEDMMP KVHWLRTQFP SLDIEVDGGV GPDTVHKCAE 190 200 210 220 AGANMIVSGS AIMRSEDPRS VINLLRNVCS EAAQKRSLDR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Thymus.
[2]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Bone marrow, Placenta and Skin.
[4]	"Characterization of 16 novel human genes showing high similarity to yeast sequences." Stanchi F., Bertocco E., Toppo S., Dioguardi R., Simionati B., Cannata N., Zimbello R., Lanfranchi G., Valle G. Yeast 18:69-80(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 55-228 (ISOFORM 1). Tissue: Spleen.
[5]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[6]	"Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE." Liang W., Ouyang S., Shaw N., Joachimiak A., Zhang R., Liu Z.J. FASEB J. 25:497-504(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEXES WITH IRON ION; D-RIBULOSE 5-PHOSPHATE AND D-XYLULOSE 5-PHOSPHATE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF SER-10; LEU-12; HIS-35; ASP-37; MET-39; HIS-70; MET-72; MET-141 AND ASP-175.
[7]	"Crystal structure of a D-ribulose-5-phosphate-3-epimerase (NP_954699) from Homo sapiens at 2.20 A resolution." Joint center for structural genomics (JCSG) Submitted (MAR-2011) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-224 IN COMPLEX WITH ZINC AND IRON IONS.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AK056028 mRNA. Translation: BAB71076.1. Frameshift.
AK093658 mRNA. Translation: BAC04212.1. Frameshift.
AK291035 mRNA. Translation: BAF83724.1.
CH471063 Genomic DNA. Translation: EAW70474.1.
BC005148 mRNA. Translation: AAH05148.2.
BC016764 mRNA. Translation: AAH16764.1.
BC072401 mRNA. Translation: AAH72401.1.
AJ224326 mRNA. Translation: CAA11895.1.

IPI

IPI00335280.
IPI00373788.

RefSeq

NP_008847.1. NM_006916.1.
NP_954699.1. NM_199229.1.

UniGene

Hs.282260.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3OVP	X-ray	1.70	A/B	1-228	[»]
3OVQ	X-ray	2.00	A/B	1-228	[»]
3OVR	X-ray	1.95	A/B	1-228	[»]
3QC3	X-ray	2.20	A/B	1-224	[»]

ProteinModelPortal

Q96AT9.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96AT9. 2 interactions.

MINT

MINT-1448309.

STRING

9606.ENSP00000352401.

Polymorphism databases

DMDM

34924986.

Proteomic databases

PaxDb

Q96AT9.

PRIDE

Q96AT9.

Protocols and materials databases

DNASU

6120.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000359429; ENSP00000352401; ENSG00000197713.

GeneID

6120.

KEGG

hsa:6120.

UCSC

uc002vdn.3. human.

Organism-specific databases

CTD

6120.

GeneCards

GC02P210867.

H-InvDB

HIX0190555.

HGNC

HGNC:10293. RPE.

HPA

HPA036499.

MIM

180480. gene.

neXtProt

NX_Q96AT9.

PharmGKB

PA34654.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG0036.

HOGENOM

HOG000259349.

HOVERGEN

HBG044821.

InParanoid

Q96AT9.

KO

K01783.

OMA

IDESGRD.

OrthoDB

EOG4F7NKV.

Enzyme and pathway databases

Reactome

REACT_111217. Metabolism.

Gene expression databases

ArrayExpress

Q96AT9.

Bgee

Q96AT9.

CleanEx

HS_RPE.

Genevestigator

Q96AT9.

GermOnline

ENSG00000197713. Homo sapiens.

Family and domain databases

Gene3D

3.20.20.70. 1 hit.

InterPro

IPR013785. Aldolase_TIM.
IPR026019. Ribul_P_3_epim.
IPR000056. Ribul_P_3_epim-like.
IPR011060. RibuloseP-bd_barrel.
[Graphical view]

PANTHER

PTHR11749. PTHR11749. 1 hit.

Pfam

PF00834. Ribul_P_3_epim. 1 hit.
[Graphical view]

PIRSF

PIRSF001461. RPE. 1 hit.

SUPFAM

SSF51366. RibP_bind_barrel. 1 hit.

TIGRFAMs

TIGR01163. rpe. 1 hit.

PROSITE

PS01085. RIBUL_P_3_EPIMER_1. 1 hit.
PS01086. RIBUL_P_3_EPIMER_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q96AT9.

GenomeRNAi

6120.

NextBio

23767.

SOURCE

Search...

Entry information

Entry name

RPE_HUMAN

Accession

Primary (citable) accession number: Q96AT9
Secondary accession number(s): A8K4S0 , O43767, Q8N215, Q96N34, Q9BSB5

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 19, 2003
Last sequence update:	December 1, 2001
Last modified:	May 1, 2013
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.