3ORF - JenaLib

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Title :   CRYSTAL STRUCTURE OF DIHYDROPTERIDINE REDUCTASE FROM DICTYOSTELIUM DISCOIDEUM

Authors :   C. Chen, N. N. Zhuang, K. H. Seo, Y. S. Park, K. H. Lee

Date :   07 Sep 10 (Deposition) - 27 Jul 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.16

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Alpha-Beta-Alpha Sandwich, Rossmann Fold, Oxidoreductase (Acting On Nadh), Nadh Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Chen, H. L. Kim, N. Zhuang, K. H. Seo, K. H. Park, C. -D. Han, Y. S. Park, K. H. Lee
Structural Insights Into The Dual Substrate Specificities O Mammalian And Dictyostelium Dihydropteridine Reductases Toward Two Stereoisomers Of Quinonoid Dihydrobiopterin
Febs Lett. V. 585 2640 2011
PubMed-ID: 21819985 | Reference-DOI: 10.1016/J.FEBSLET.2011.07.018

Molecule 1 - DIHYDROPTERIDINE REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.5.1.34
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	DDB_G0272684, QDPR
	Organism Common	:	SLIME MOLD
	Organism Scientific	:	DICTYOSTELIUM DISCOIDEUM
	Organism Taxid	:	44689
	Synonym	:	QUINOID DIHYDROPTERIDINE REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:8 , GLY A:12 , ALA A:13 , LEU A:14 , ASP A:33 , PHE A:34 , ARG A:35 , SER A:49 , ALA A:74 , ALA A:75 , GLY A:76 , GLY A:77 , ASP A:97 , MET A:98 , ASN A:99 , SER A:102 , GLY A:124 , ALA A:125 , TYR A:138 , LYS A:142 , PRO A:170 , VAL A:171 , THR A:172 , LEU A:173 , THR A:175 , ASN A:178 , HOH A:253 , HOH A:269	BINDING SITE FOR RESIDUE NAD A 901
2	AC2	SOFTWARE	GLY B:12 , ALA B:13 , LEU B:14 , ASP B:33 , PHE B:34 , ARG B:35 , SER B:49 , ALA B:74 , ALA B:75 , GLY B:76 , GLY B:77 , ASP B:97 , MET B:98 , THR B:123 , GLY B:124 , TYR B:138 , LYS B:142 , PRO B:170 , LEU B:173 , THR B:175 , ASN B:178 , HOH B:236 , HOH B:239 , HOH B:242	BINDING SITE FOR RESIDUE NAD B 902
3	AC3	SOFTWARE	LEU C:8 , GLY C:12 , ALA C:13 , LEU C:14 , ASP C:33 , PHE C:34 , ARG C:35 , SER C:49 , ALA C:74 , ALA C:75 , GLY C:76 , GLY C:77 , ASP C:97 , MET C:98 , THR C:123 , GLY C:124 , TYR C:138 , LYS C:142 , PRO C:170 , VAL C:171 , THR C:172 , LEU C:173 , THR C:175 , HOH C:232 , HOH C:262 , SER D:183 , ASP D:184	BINDING SITE FOR RESIDUE NAD C 903
4	AC4	SOFTWARE	SER C:183 , ASP C:184 , LEU D:8 , GLY D:12 , ALA D:13 , LEU D:14 , ASP D:33 , PHE D:34 , ARG D:35 , SER D:49 , ALA D:74 , ALA D:75 , GLY D:76 , GLY D:77 , ASP D:97 , MET D:98 , SER D:102 , THR D:123 , GLY D:124 , TYR D:138 , LYS D:142 , PRO D:170 , THR D:172 , LEU D:173 , ASN D:178 , HOH D:236 , HOH D:255	BINDING SITE FOR RESIDUE NAD D 904

(no "SS Bond" information available for 3ORF)

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

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHPR_DICDI	125-153	4	A:125-153 B:125-153 C:125-153 D:125-153

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	DHPR_DICDI	125-153	2	A:125-153 B:125-153 - -

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.	DHPR_DICDI	125-153	2	- - C:125-153 D:125-153

(no "Exon" information available for 3ORF)

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:230
 aligned with DHPR_DICDI | Q86A17 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           DHPR_DICDI     2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
               SCOP domains d3orfa_ A: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee........eeee....hhhhhhhhhhhhhh....eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........eeeeeee....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:125-153    ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3orf A   2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain B from PDB  Type:PROTEIN  Length:230
 aligned with DHPR_DICDI | Q86A17 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           DHPR_DICDI     2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
               SCOP domains d3orfb_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee........eeee....hhhhhhhhhhhhh.....eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:125-153    ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3orf B   2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain C from PDB  Type:PROTEIN  Length:230
 aligned with DHPR_DICDI | Q86A17 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           DHPR_DICDI     2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
               SCOP domains d3orfc_ C: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee........eeee....hhhhhhhhhhhhhh....eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhhhh.........eeeeeee....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:125-153    ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3orf C   2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain D from PDB  Type:PROTEIN  Length:230
 aligned with DHPR_DICDI | Q86A17 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           DHPR_DICDI     2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
               SCOP domains d3orfd_ D: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhh...eeeeee........eeee....hhhhhhhhhhhhhh....eeeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.hhhhhh....hhhhhhhhhhhhhhhhhh...........eeeeeee..eehhhhhhhh...hhhhheehhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:125-153    ------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3orf D   2 SKNILVLGGSGALGAEVVKFFKSKSWNTISIDFRENPNADHSFTIKDSGEEEIKSVIEKINSKSIKVDTFVCAAGGWSGGNASSDEFLKSVKGMIDMNLYSAFASAHIGAKLLNQGGLFVLTGASAALNRTSGMIAYGATKAATHHIIKDLASENGGLPAGSTSLGILPVTLDTPTNRKYMSDANFDDWTPLSEVAEKLFEWSTNSDSRPTNGSLVKFETKSKVTTWTNL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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: automated matches (447)

Protein domain: automated matches (447)

Slime mold (Dictyostelium discoideum) [TaxId: 44689] (1)

1a	d3orfa_	A:
1b	d3orfb_	B:
1c	d3orfc_	C:
1d	d3orfd_	D:

(no "CATH Domain" information available for 3ORF)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DHPR_DICDI | Q86A17)

molecular function
	GO:0004155	6,7-dihydropteridine reductase activity	Catalysis of the reaction: NADP+ + 5,6,7,8-tetrahydropteridine = NADPH + H+ + 6,7-dihydropteridine.
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	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:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
	GO:0044351	macropinocytosis	An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
	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:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
	GO:0006729	tetrahydrobiopterin biosynthetic process	The chemical reactions and pathways resulting in the formation of tetrahydrobiopterin, the reduced form of biopterin (2-amino-4-hydroxy-6-(1,2-dihydroxypropyl)-pteridine). It functions as a hydroxylation coenzyme, e.g. in the conversion of phenylalanine to tyrosine.
cellular component
	GO:0045335	phagocytic vesicle	A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3orf)

Biological Units
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	1.5.1.34
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1dhr	THE SAME PROTEIN COMPLEXED WITH NAD
1dir	THE SAME PROTEIN COMPLEXED WITH NAD
1hdr	THE SAME PROTEIN COMPLEXED WITH NAD
1ooe	THE SAME PROTEIN

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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