3DOJ - JenaLib

Title :   STRUCTURE OF GLYOXYLATE REDUCTASE 1 FROM ARABIDOPSIS (ATGLYR1)

Authors :   R. Jorgensen

Date :   04 Jul 08 (Deposition) - 07 Jul 09 (Release) - 07 Jul 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Gamma-Hydroxybutyrate Dehydrogenase, 4-Hydroxybutyrate Dehydrogenase, Succinic Semialdehyde Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Hoover, R. Jorgensen, A. R. Merrill, B. J. Shelp
Cytosolic Nadph-Dependent Glyoxylate Reductase From Arabidopsis: Crystal Structure And Kinetic Characterization Of Active Site Mutants
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:292
 aligned with GLYR1_ARATH | Q9LSV0 from UniProtKB/Swiss-Prot  Length:289

    Alignment length:292
                                1                                                                                                                                                                                                                                                                                               
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
          GLYR1_ARATH     - ----MEVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIAMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSGSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMNAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVKFSR 288
               SCOP domains d3doja1 A:-3-162 automated matches                                                                                                                                    d3doja2 A:163-288 automated matches                                                                                            SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhh..ee..hhhhhhhhh.eeee...hhhhhhhhhhh..hhhhhh....eeee....hhhhhhhhhhhhhhh..eeee..ee.hhhhhhhh.eeeeeeehhhhhhhhhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------3_HYDROXYISOBU------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3doj A  -3 GSHMMEVGFLGLGIMGKAMSMNLLKNGFKVTVWNRTLSKCDELVEHGASVCESPAEVIKKCKYTIAMLSDPCAALSVVFDKGGVLEQICEGKGYIDMSTVDAETSLKINEAITGKGGRFVEGPVSGSKKPAEDGQLIILAAGDKALFEESIPAFDVLGKRSFYLGQVGNGAKMKLIVNMIMGSMMNAFSEGLVLADKSGLSSDTLLDILDLGAMTNPMFKGKGPSMNKSSYPPAFPLKHQQKDMRLALALGDENAVSMPVAAAANEAFKKARSLGLGDLDFSAVIEAVKFSR 288
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric Unit(hide GO term definitions)

Chain A (GLYR1_ARATH | Q9LSV0)

molecular function
	GO:0003858	3-hydroxybutyrate dehydrogenase activity	Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD(+) = acetoacetate + H(+) + NADH.
	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:0030267	glyoxylate reductase (NADP) activity	Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
	GO:0004616	phosphogluconate dehydrogenase (decarboxylating) activity	Catalysis of the reaction: 6-phospho-D-gluconate + NADP+ = D-ribulose 5-phosphate + CO2 + NADPH + H+.
biological process
	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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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