1QYD - JenaLib

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Title :   CRYSTAL STRUCTURES OF PINORESINOL-LARICIRESINOL AND PHENYLCOUMARAN BENZYLIC ETHER REDUCTASES, AND THEIR RELATIONSHIP TO ISOFLAVONE REDUCTASES

Authors :   T. Min, H. Kasahara, D. L. Bedgar, B. Youn, P. K. Lawrence, D. R. Gang, S. C. Halls, H. Park, J. L. Hilsenbeck, L. B. Davin, C. Kang

Date :   10 Sep 03 (Deposition) - 04 Nov 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Nadph-Dependent Aromatic Alcohol Reductases, Pcber, Plr, Ifr, Lignans, Isoflavonoids, Plant Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Min, H. Kasahara, D. L. Bedgar, B. Youn, P. K. Lawrence, D. R. Gang, S. C. Halls, H. Park, J. L. Hilsenbeck, L. B. Davin, N. G. Lewis, C. Kang
Crystal Structures Of Pinoresinol-Lariciresinol And Phenylcoumaran Benzylic Ether Reductases And Their Relationship To Isoflavone Reductases.
J. Biol. Chem. V. 278 50714 2003
PubMed-ID: 13129921 | Reference-DOI: 10.1074/JBC.M308493200
(for further references see the PDB file header)

Molecule 1 - PINORESINOL-LARICIRESINOL REDUCTASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	469008
	Organism Common	:	GIANT ARBORVITAE
	Organism Scientific	:	THUJA PLICATA
	Organism Taxid	:	3316

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QYD)

(no "Site" information available for 1QYD)

(no "SS Bond" information available for 1QYD)

Asymmetric Unit

No.	Residues
1	Gln A:129	-	Pro A:130
2	Gln B:129	-	Pro B:130
3	Gln C:129	-	Pro C:130
4	Gln D:129	-	Pro D:130

(no "SAP(SNP)/Variant" information available for 1QYD)

(no "PROSITE Motif" information available for 1QYD)

(no "Exon" information available for 1QYD)

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:312
 aligned with PILR1_THUPL | Q9LD14 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
          PILR1_THUPL     2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
               SCOP domains d1qyda_ A: Pinoresinol-lariciresinol reductase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1qydA01 A:2-156,A:197-219,A:285-297 NAD(P)-binding Rossmann-like Domain                                                                                    1qydA02 A:157-196,A:220-284,A:298-313   1qydA01                1qydA02 A:157-196,A:220-284,A:298-313                            1qydA01      1qydA02          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhh...eee.....hhhhhhhhhh...eeee............hhhhhhhhhhhh....eee..................hhhhhhhhhhhhhhhhh.....eee..eehhhhh...............ee........eeeeehhhhhhhhhhhhh.hhhhh..eee..hhh.eeehhhhhhhhhhhhh...ee....hhhhhhhhh....hhhhhh.hhhhhh.............eeehhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyd A   2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:312
 aligned with PILR1_THUPL | Q9LD14 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
          PILR1_THUPL     2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
               SCOP domains d1qydb_ B: Pinoresinol-lariciresinol reductase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1qydB01 B:2-156,B:197-219,B:285-297 NAD(P)-binding Rossmann-like Domain                                                                                    1qydB02 B:157-196,B:220-284,B:298-313   1qydB01                1qydB02 B:157-196,B:220-284,B:298-313                            1qydB01      1qydB02          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhheeee.....hhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh....eee.................hhhhhhhhhhhhh.........eeee..ee....................eeee.......eeeehhhhhhhhhhhhhhhhhhh.eeee..hhh.eehhhhhhhhhh.......eeee..hhhhhhh....hhhhhhhhhhhhhhh.............eeehhhhh......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyd B   2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain C from PDB  Type:PROTEIN  Length:312
 aligned with PILR1_THUPL | Q9LD14 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
          PILR1_THUPL     2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
               SCOP domains d1qydc_ C: Pinoresinol-lariciresinol reductase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1qydC01 C:2-156,C:197-219,C:285-297 NAD(P)-binding Rossmann-like Domain                                                                                    1qydC02 C:157-196,C:220-284,C:298-313   1qydC01                1qydC02 C:157-196,C:220-284,C:298-313                            1qydC01      1qydC02          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhh.eeee....hhhhhhhhhh...eeee............hhhhhhhhhh..........................hhhhhhhhhhhhhhhhhh.....eee..eehhhhh...............eeeee.....eeeeehhhhhhhhhhh..........eee..hhh.eeehhhhhhhhh.......eeeee.hhhhhhhhhhhhhhhhhhhhhhh.................eehhhhh..........hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyd C   2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain D from PDB  Type:PROTEIN  Length:312
 aligned with PILR1_THUPL | Q9LD14 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:312
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311  
          PILR1_THUPL     2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
               SCOP domains d1qydd_ D: Pinoresinol-lariciresinol reductase                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1qydD01 D:2-156,D:197-219,D:285-297 NAD(P)-binding Rossmann-like Domain                                                                                    1qydD02 D:157-196,D:220-284,D:298-313   1qydD01                1qydD02 D:157-196,D:220-284,D:298-313                            1qydD01      1qydD02          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee.....hhhhhhhhhhhh...eee........hhhhhhhhhhhhhhh.........hhhhhhhhh....eeee.......hhhhhh......hhhhhh...eee.................hhhhhhhhhhhhhhhhhh.....eee..eehhhhh...............eee.......eeeeehhhhhhhhhhhhh........eee..hhh.eeehhhhhhhhhhhhh...eee.....hhhhhhhhh..hhhhhhhhhh.................eehhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1qyd D   2 DKKSRVLIVGGTGYIGKRIVNASISLGHPTYVLFRPEVVSNIDKVQMLLYFKQLGAKLIEASLDDHQRLVDALKQVDVVISALAGGVLSHHILEQLKLVEAIKEAGNIKRFLPSEFGMDPDIMEHALQPGSITFIDKRKVRRAIEAASIPYTYVSSNMFAGYFAGSLAQLDGHMMPPRDKVLIYGDGNVKGIWVDEDDVGTYTIKSIDDPQTLNKTMYIRPPMNILSQKEVIQIWERLSEQNLDKIYISSQDFLADMKDKSYEEKIVRCHLYQIFFRGDLYNFEIGPNAIEATKLYPEVKYVTMDSYLERYV 313
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

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: Tyrosine-dependent oxidoreductases (503)

Protein domain: Pinoresinol-lariciresinol reductase (1)

Giant arborvitae (Thuja plicata) [TaxId: 3316] (1)

1a	d1qyda_	A:
1b	d1qydb_	B:
1c	d1qydc_	C:
1d	d1qydd_	D:

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)

Giant arborvitae (Thuja plicata) (1)

1a	1qydA01	A:2-156,A:197-219,A:285-297
1b	1qydB01	B:2-156,B:197-219,B:285-297
1c	1qydC01	C:2-156,C:197-219,C:285-297
1d	1qydD01	D:2-156,D:197-219,D:285-297

Architecture: Alpha-Beta Complex (3881)

Topology: UDP-galactose 4-epimerase; domain 1 (99)

Homologous Superfamily: UDP-galactose 4-epimerase, domain 1 (99)

Giant arborvitae (Thuja plicata) (1)

2a	1qydA02	A:157-196,A:220-284,A:298-313
2b	1qydB02	B:157-196,B:220-284,B:298-313
2c	1qydC02	C:157-196,C:220-284,C:298-313
2d	1qydD02	D:157-196,D:220-284,D:298-313

(no "Pfam Domain" information available for 1QYD)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PILR1_THUPL | Q9LD14)

molecular function
	GO:0010284	lariciresinol reductase activity	Catalysis of the reaction: lariciresinol + NADPH + H+ = secoisolariciresinol + NADP+.
	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:0010283	pinoresinol reductase activity	Catalysis of the reaction: pinoresinol + NADPH + H+ = lariciresinol + NADP+.
biological process
	GO:1902132	(+)-lariciresinol biosynthetic process	The chemical reactions and pathways resulting in the formation of (+)-lariciresinol.
	GO:1902125	(+)-pinoresinol catabolic process	The chemical reactions and pathways resulting in the breakdown of (+)-pinoresinol.
	GO:1902135	(+)-secoisolariciresinol biosynthetic process	The chemical reactions and pathways resulting in the formation of (+)-secoisolariciresinol.
	GO:1902129	(-)-lariciresinol biosynthetic process	The chemical reactions and pathways resulting in the formation of (-)-lariciresinol.
	GO:1902128	(-)-lariciresinol catabolic process	The chemical reactions and pathways resulting in the breakdown of (-)-lariciresinol.
	GO:1902123	(-)-pinoresinol catabolic process	The chemical reactions and pathways resulting in the breakdown of (-)-pinoresinol.
	GO:0009807	lignan biosynthetic process	The chemical reactions and pathways resulting in the formation of lignans, any member of a class of plant metabolites related to lignins. Lignans are usually found as phenylpropanoid dimers in which the phenylpropanoid units are linked tail to tail and thus having a 2,3 dibenzylbutane skeleton, but higher oligomers can also exist.
	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.

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	Cis Peptide Bonds
		Gln A:129 - Pro A:130	[ RasMol ]
		Gln B:129 - Pro B:130	[ RasMol ]
		Gln C:129 - Pro C:130	[ RasMol ]
		Gln D:129 - Pro D:130	[ RasMol ]

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