EzCatDB: S00602
Related links:    PDB-formatted query search system Fasta-formatted query search system Fasta-formatted query search system

DB codeS00602
RLCP classification9.5010.536200.8010 : Hydride transfer
CATH domainDomain 13.40.50.720 : Rossmann foldCatalytic domain
E.C.1.1.1.10

CATH domainRelated DB codes (homologues)
3.40.50.720 : Rossmann foldS00543,S00551,S00552,S00553,S00604,S00605,S00608,S00610,S00625,S00319,S00328,S00329,S00330,S00331,S00332,D00456,D00457,D00458,S00324,S00320,S00325,S00326,S00327,D00459,S00335,S00336,S00334,T00219,S00339,D00513,D00001,D00002,D00003,D00005,D00007,D00008,D00010,D00012,D00017,D00018,D00023,D00027,D00028,D00031,D00032,D00033,D00034,D00035,D00037,D00048,D00071,D00476,D00481,D00482,D00490,D00492,D00494,D00545,D00601,D00603,D00604,D00605,D00615,D00845,D00857,D00858,M00161,M00171,M00210,T00002,T00010,T00011,T00015,T00227,T00247,T00408,T00414,D00827,D00262,D00274,D00275,M00035,T00109

Enzyme Name
UniProtKBKEGG

Q7Z4W1
Protein nameL-xylulose reductaseL-Xylulose reductase
Xylitol dehydrogenase
SynonymsXR
EC 1.1.1.10
Dicarbonyl/L-xylulose reductase
Kidney dicarbonyl reductase
kiDCR
Carbonyl reductase II
Sperm surface protein P34H
RefSeqNP_001182147.1 (Protein)
NM_001195218.1 (DNA/RNA sequence)
NP_057370.1 (Protein)
NM_016286.3 (DNA/RNA sequence)

KEGG pathways
MAP codePathways
MAP00040Pentose and glucuronate interconversions

UniProtKB:Accession NumberQ7Z4W1
Entry nameDCXR_HUMAN
ActivityXylitol + NADP(+) = L-xylulose + NADPH.
SubunitHomotetramer.
Subcellular locationMembrane, peripheral membrane protein (By similarity). Probably recruited to membranes via an interaction with phosphatidylinositol (By similarity).
Cofactor

Compound table: links to PDB-related databases & PoSSuM

SubstratesProducts
KEGG-idC00312C00005C00080C00379C00006
CompoundL-xyluloseNADPHH+xylitolNADP+
Typecarbohydrateamide group,amine group,nucleotideotherscarbohydrateamide group,amine group,nucleotide
ChEBI
16474
15378
17151
18009
PubChem439205
5884
1038

5886
             
1pr9A00UnboundUnbound UnboundBound:NAP
1pr9B00UnboundUnbound UnboundBound:NAP
1wntA00UnboundUnbound UnboundBound:NAP
1wntB00UnboundUnbound UnboundBound:NAP
1wntC00UnboundUnbound UnboundBound:NAP
1wntD00UnboundUnbound UnboundBound:NAP
3d3wA00UnboundUnbound UnboundBound:NAP
3d3wB00UnboundUnbound UnboundBound:NAP

Active-site residues
resource
literature;[4], [6], [7]
pdbCatalytic residues
         
1pr9A00SER 136;TYR 149;LYS 153
1pr9B00SER 136;TYR 149;LYS 153
1wntA00SER 136;TYR 149;LYS 153
1wntB00SER 136;TYR 149;LYS 153
1wntC00SER 136;TYR 149;LYS 153
1wntD00SER 136;TYR 149;LYS 153
3d3wA00SER 136;TYR 149;LYS 153
3d3wB00SER 136;TYR 149;LYS 153

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[4]p.545-6, Table.1
[6]p.729-31
[7]p.431, Fig.7

references
[1]
PubMed ID8805511
JournalStructure
Year1996
Volume4
Pages33-45
AuthorsTanaka N, Nonaka T, Nakanishi M, Deyashiki Y, Hara A, Mitsui Y
TitleCrystal structure of the ternary complex of mouse lung carbonyl reductase at 1.8 A resolution: the structural origin of coenzyme specificity in the short-chain dehydrogenase/reductase family.
[2]
CommentsX-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS).
PubMed ID12136162
JournalActa Crystallogr D Biol Crystallogr
Year2002
Volume58
Pages1379-80
AuthorsEl-Kabbani O, Chung RP, Ishikura S, Usami N, Nakagawa J, Hara A
TitleCrystallization and preliminary crystallographic analysis of human L-xylulose reductase.
Related UniProtKBQ7Z4W1
[3]
PubMed ID11882650
JournalJ Biol Chem
Year2002
Volume277
Pages17883-91
AuthorsNakagawa J, Ishikura S, Asami J, Isaji T, Usami N, Hara A, Sakurai T, Tsuritani K, Oda K, Takahashi M, Yoshimoto M, Otsuka N, Kitamura K
TitleMolecular characterization of mammalian dicarbonyl/L-xylulose reductase and its localization in kidney.
[4]
PubMed ID12604240
JournalChem Biol Interact
Year2003
Volume143-144
Pages543-50
AuthorsIshikura S, Isaji T, Usami N, Nakagawa J, El-Kabbani O, Hara A
TitleIdentification of amino acid residues involved in substrate recognition of L-xylulose reductase by site-directed mutagenesis.
[5]
PubMed ID12604210
JournalChem Biol Interact
Year2003
Volume143-144
Pages247-53
AuthorsOppermann U, Filling C, Hult M, Shafqat N, Wu X, Lindh M, Shafqat J, Nordling E, Kallberg Y, Persson B, Jornvall H
TitleShort-chain dehydrogenases/reductases (SDR): the 2002 update.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) IN COMPLEX WITH NADP AND SUBSTRATE, AND MUTAGENESIS OF ASN-107.
PubMed ID15103634
JournalProteins
Year2004
Volume55
Pages724-32
AuthorsEl-Kabbani O, Ishikura S, Darmanin C, Carbone V, Chung RP, Usami N, Hara A
TitleCrystal structure of human L-xylulose reductase holoenzyme: probing the role of Asn107 with site-directed mutagenesis.
Related PDB1pr9
Related UniProtKBQ7Z4W1
[7]
CommentsX-RAY CRYSTALLOGRAPHY
PubMed ID15906319
JournalProteins
Year2005
Volume60
Pages424-32
AuthorsEl-Kabbani O, Carbone V, Darmanin C, Ishikura S, Hara A
TitleStructure of the tetrameric form of human L-Xylulose reductase: probing the inhibitor-binding site with molecular modeling and site-directed mutagenesis.
Related PDB1wnt
[8]
PubMed ID19337691
JournalCell Mol Life Sci
Year2009
Volume66
Pages1570-9
AuthorsZhao HT, Endo S, Ishikura S, Chung R, Hogg PJ, Hara A, El-Kabbani O
TitleStructure/function analysis of a critical disulfide bond in the active site of L-xylulose reductase.
Related PDB3d3w

comments
This enzyme belongs to the short-chain dehydrogenase/reductase (SDR) superfamily, along with Drosophia alcohol dehydrogenase (S00319 in EzCatDB). This enzyme has got a catalytic triad composed of conserved residues, Ser, Tyr, and Lys. The conformation of these residues, compared to that of the NAD molecule, seems to be similar to that of the homologous enzymes. Thus, this enzyme catalyzes hydride transfer reaction from NADH to substrate.
Moreover, there is a disulfide bond between Cys138 and Cys150, whose conformation seems to be structurally unstable, near the active site (see [8]). This property is very unique to this enzyme, compared to the other homologous enzymes. The disulfide bond might be involved in regulation of the enzyme activity, through its S-cysteinylation (see [8]).

createdupdated
2008-11-052011-07-19


Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2012 - March 2013)
Supported by the commission for the Development of Artificial Gene Synthesis Technology for Creating Innovative Biomaterial from the Ministry of Economy, Trade and Industry (METI) (October 2012 - )
© Biotechnology Research Institute for Drug Discovery, AIST, 2015-2016 All Rights Reserved.
© Computational Biology Research Center, AIST, 2004-2016 All Rights Reserved.