3D3W - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   STRUCTURE OF L-XYLULOSE REDUCTASE WITH BOUND COENZYME, PHOSPHATE AND HYDROXIDE.

Authors :   H. -T. Zhao, O. El-Kabbani

Date :   12 May 08 (Deposition) - 21 Apr 09 (Release) - 28 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)
Biol. Unit 2: A (1x),B (1x)
Biol. Unit 3: A  (2x)
Biol. Unit 4: B  (2x)

Keywords :   L-Xylulose Reductase, Uronate Cycle, Short-Chain Dehydrogenase/Reductase(Sdr) Superfamily, Glucose Metabolism, Acetylation, Carbohydrate Metabolism, Membrane, Nadp, Oxidoreductase, Xylose Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. T. Zhao, S. Endo, S. Ishikura, R. Chung, P. J. Hogg, A. Hara, O. El-Kabbani
Structure/Function Analysis Of A Critical Disulfide Bond In The Active Site Of L-Xylulose Reductase.
Cell. Mol. Life Sci. V. 66 1570 2009
PubMed-ID: 19337691 | Reference-DOI: 10.1007/S00018-009-9065-Y
(for further references see the PDB file header)

Molecule 1 - L-XYLULOSE REDUCTASE
	Chains	:	A
	EC Number	:	1.1.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCXR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CSO AT POSITION 138
	Synonym	:	XR, DICARBONYL/L-XYLULOSE REDUCTASE, KIDNEY DICARBONYL REDUCTASE, KIDCR, CARBONYL REDUCTASE II, SPERM SURFACE PROTEIN P34H

Molecule 2 - L-XYLULOSE REDUCTASE
	Chains	:	B
	EC Number	:	1.1.1.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DCXR
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	CYS/CSO AT POSITION 138
	Synonym	:	XR, DICARBONYL/L-XYLULOSE REDUCTASE, KIDNEY DICARBONYL REDUCTASE, KIDCR, CARBONYL REDUCTASE II, SPERM SURFACE PROTEIN P34H

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (1x)	:	A (1x)	B (1x)
Biological Unit 3 (2x)	:	A
Biological Unit 4 (2x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	CSO	4	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	CSO	1	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PO4	-1	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (3, 6)

No.	Name	Count	Type	Full Name
1	CSO	2	Mod. Amino Acid	S-HYDROXYCYSTEINE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , GLY A:16 , LYS A:17 , GLY A:18 , ILE A:19 , SER A:38 , ARG A:39 , THR A:40 , ASP A:43 , VAL A:59 , ASP A:60 , LEU A:61 , GLY A:62 , ASN A:83 , ALA A:84 , ALA A:85 , VAL A:86 , ARG A:102 , VAL A:106 , VAL A:134 , SER A:135 , SER A:136 , TYR A:149 , LYS A:153 , PRO A:179 , THR A:180 , VAL A:182 , THR A:184 , SER A:185 , MET A:186 , GLY A:187 , HOH A:259 , HOH A:263 , HOH A:270 , HOH A:295 , HOH A:297 , HOH A:367	BINDING SITE FOR RESIDUE NAP A 245
2	AC2	SOFTWARE	GLY B:14 , GLY B:16 , LYS B:17 , GLY B:18 , ILE B:19 , SER B:38 , ARG B:39 , THR B:40 , ASP B:43 , VAL B:59 , ASP B:60 , LEU B:61 , GLY B:62 , ASN B:83 , ALA B:84 , ALA B:85 , ARG B:102 , VAL B:106 , VAL B:134 , SER B:135 , SER B:136 , TYR B:149 , LYS B:153 , PRO B:179 , THR B:180 , VAL B:181 , VAL B:182 , THR B:184 , SER B:185 , GLY B:187 , PO4 B:245 , HOH B:1250 , HOH B:1281 , HOH B:1307 , HOH B:1319 , HOH B:1345 , HOH B:1362 , HOH B:1410 , HOH B:1439	BINDING SITE FOR RESIDUE NAP B 1245
3	AC3	SOFTWARE	SER B:136 , GLN B:137 , CYS B:138 , PRO B:179 , THR B:180 , VAL B:181 , MET B:200 , NAP B:1245 , HOH B:1439	BINDING SITE FOR RESIDUE PO4 B 245

Asymmetric Unit

No.	Residues
1	B:138	-	B:150

(no "Cis Peptide Bond" information available for 3D3W)

(no "SAP(SNP)/Variant" information available for 3D3W)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DCXR_HUMAN	136-164	2	A:136-164 B:136-164

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DCXR_HUMAN	136-164	4	A:136-164 B:136-164

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DCXR_HUMAN	136-164	2	A:136-164 B:136-164

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DCXR_HUMAN	136-164	2	A:136-164 -

Biological Unit 4 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DCXR_HUMAN	136-164	2	- B:136-164

Asymmetric Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000306869	1	ENSE00001155492	chr17:79995573-79995507	67	DCXR_HUMAN	1-18	18	2	A:1-18 B:1-18	18 18
1.2	ENST00000306869	2	ENSE00001164074	chr17:79995423-79995326	98	DCXR_HUMAN	18-50	33	2	A:18-50 B:18-50	33 33
1.3	ENST00000306869	3	ENSE00001164069	chr17:79994889-79994735	155	DCXR_HUMAN	51-102	52	2	A:51-102 B:51-102	52 52
1.4	ENST00000306869	4	ENSE00001164064	chr17:79994639-79994597	43	DCXR_HUMAN	102-116	15	2	A:102-116 B:102-116	15 15
1.5	ENST00000306869	5	ENSE00001164060	chr17:79994519-79994420	100	DCXR_HUMAN	117-150	34	2	A:117-150 B:117-150	34 34
1.6	ENST00000306869	6	ENSE00001164055	chr17:79994324-79994260	65	DCXR_HUMAN	150-171	22	2	A:150-171 B:150-171	22 22
1.7	ENST00000306869	7	ENSE00001164049	chr17:79994184-79994067	118	DCXR_HUMAN	172-211	40	2	A:172-211 B:172-211	40 40
1.8	ENST00000306869	8	ENSE00001300238	chr17:79993939-79993757	183	DCXR_HUMAN	211-244	34	2	A:211-244 B:211-244	34 34

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:244
 aligned with DCXR_HUMAN | Q7Z4W1 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           DCXR_HUMAN     1 MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC 244
               SCOP domains d3d3wa_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3d3wA00 A:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee....hhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:136-164    -------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1          --------------------------------Exon 1.3  PDB: A:51-102 UniProt: 51-102             --------------Exon 1.5  PDB: A:117-150          ---------------------Exon 1.7  PDB: A:172-211                --------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.2  PDB: A:18-50           ---------------------------------------------------Exon 1.4       ---------------------------------Exon 1.6              ---------------------------------------Exon 1.8  PDB: A:211-244           Transcript 1 (2)
                 3d3w A   1 MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQcSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
                                                                                                                                                                   138-CSO

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with DCXR_HUMAN | Q7Z4W1 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           DCXR_HUMAN     1 MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC 244
               SCOP domains d3d3wb_ B: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains 3d3wB00 B:1-244 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeee....hhhhhhhhhh......eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:136-164    -------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1          --------------------------------Exon 1.3  PDB: B:51-102 UniProt: 51-102             --------------Exon 1.5  PDB: B:117-150          ---------------------Exon 1.7  PDB: B:172-211                --------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.2  PDB: B:18-50           ---------------------------------------------------Exon 1.4       ---------------------------------Exon 1.6              ---------------------------------------Exon 1.8  PDB: B:211-244           Transcript 1 (2)
                 3d3w B   1 MELFLAGRRVLVTGAGKGIGRGTVQALHATGARVVAVSRTQADLDSLVRECPGIEPVCVDLGDWEATERALGSVGPVDLLVNNAAVALLQPFLEVTKEAFDRSFEVNLRAVIQVSQIVARGLIARGVPGAIVNVSSQCSQRAVTNHSVYCSTKGALDMLTKVMALELGPHKIRVNAVNPTVVMTSMGQATWSDPHKAKTMLNRIPLGKFAEVEHVVNAILFLLSDRSGMTTGSTLPVEGGFWAC 244
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: automated matches (114)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d3d3wa_	A:
1b	d3d3wb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

1a	3d3wA00	A:1-244
1b	3d3wB00	B:1-244

(no "Pfam Domain" information available for 3D3W)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCXR_HUMAN | Q7Z4W1)

molecular function
	GO:0050038	L-xylulose reductase (NADP+) activity	Catalysis of the reaction: NADP(+) + xylitol = L-xylulose + H(+) + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
biological process
	GO:0042732	D-xylose metabolic process	The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.
	GO:0006739	NADP metabolic process	The chemical reactions and pathways involving nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; metabolism may be of either the oxidized form, NADP, or the reduced form, NADPH.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	GO:0019640	glucuronate catabolic process to xylulose 5-phosphate	The chemical reactions and pathways resulting in the breakdown of glucuronate into other compounds, including xylulose 5-phosphate.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0005997	xylulose metabolic process	The chemical reactions and pathways involving xylulose, the ketopentose threo-2-pentulose.
cellular component
	GO:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	GO:0005881	cytoplasmic microtubule	Any microtubule in the cytoplasm of a cell.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005902	microvillus	Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
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	3d3w
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	DCXR_HUMAN \| Q7Z4W1	:	1pr9 1wnt

1pr9	SAME PROTEIN WITH DISULFIDE BOND PRESENT IN THE ACTIVE SITE, ALONG WITH BOUND PHOSPHATE.

Description

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Ligands, Modified Residues, Ions (3, 5)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

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Exons (8, 16)

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