3H7R - JenaLib

Title :   CRYSTAL STRUCTURE OF THE PLANT STRESS-RESPONSE ENZYME AKR4C8

Authors :   S. A. White, P. J. Simpson, J. P. Ride

Date :   28 Apr 09 (Deposition) - 04 Aug 09 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

Chains :   Asym./Biol. Unit : A

Keywords :   Stress Response, Aldo-Keto Reductase, Nadp, Drought Tolerance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Simpson, C. Tantitadapitak, A. M. Reed, O. C. Mather, C. M. Bunce, S. A. White, J. P. Ride
Characterization Of Two Novel Aldo-Keto Reductases From Arabidopsis: Expression Patterns, Broad Substrate Specificity, And An Open Active-Site Structure Suggest A Role In Toxicant Metabolism Following Stress.
J. Mol. Biol. V. 392 465 2009
PubMed-ID: 19616008 | Reference-DOI: 10.1016/J.JMB.2009.07.023
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:22 , THR A:23 , TYR A:24 , ASP A:43 , TYR A:48 , HIS A:110 , SER A:154 , ASN A:155 , GLN A:176 , TYR A:202 , SER A:203 , PRO A:204 , LEU A:205 , GLY A:206 , SER A:207 , GLN A:208 , ARG A:214 , ALA A:235 , LEU A:250 , PRO A:251 , LYS A:252 , SER A:253 , SER A:254 , ARG A:258 , GLU A:261 , ASN A:262 , ACT A:501 , HOH A:637 , HOH A:836 , HOH A:839 , HOH A:972 , HOH A:993 , HOH A:1002	BINDING SITE FOR RESIDUE NAP A 401
02	AC2	SOFTWARE	TYR A:24 , TYR A:48 , HIS A:110 , NAP A:401 , HOH A:692 , HOH A:951	BINDING SITE FOR RESIDUE ACT A 501
03	AC3	SOFTWARE	PRO A:17 , CYS A:18 , VAL A:19 , ARG A:40 , HIS A:41 , HOH A:787	BINDING SITE FOR RESIDUE EDO A 502
04	AC4	SOFTWARE	GLN A:185 , GLY A:187 , LEU A:188 , GLU A:310 , HOH A:652 , HOH A:710	BINDING SITE FOR RESIDUE EDO A 503
05	AC5	SOFTWARE	THR A:123 , PRO A:124 , THR A:290 , GLU A:291 , ALA A:293 , HIS A:294 , HOH A:747 , HOH A:997	BINDING SITE FOR RESIDUE EDO A 504
06	AC6	SOFTWARE	LYS A:15 , LEU A:72 , PHE A:73 , HOH A:633 , HOH A:739 , HOH A:926	BINDING SITE FOR RESIDUE EDO A 505
07	AC7	SOFTWARE	ILE A:35 , LYS A:36 , ILE A:37 , GLY A:38 , ARG A:40 , PHE A:66 , HOH A:734 , HOH A:768 , HOH A:948	BINDING SITE FOR RESIDUE EDO A 506
08	AC8	SOFTWARE	ALA A:141 , LYS A:216 , EDO A:508 , HOH A:845 , HOH A:920 , HOH A:953	BINDING SITE FOR RESIDUE EDO A 507
09	AC9	SOFTWARE	GLU A:140 , ALA A:141 , ASP A:144 , ARG A:169 , LYS A:216 , EDO A:507 , HOH A:676 , HOH A:766 , HOH A:958	BINDING SITE FOR RESIDUE EDO A 508
10	BC1	SOFTWARE	GLU A:9 , ASN A:11 , LYS A:52 , GLY A:196 , HOH A:703	BINDING SITE FOR RESIDUE EDO A 509
11	BC2	SOFTWARE	GLU A:125 , GLU A:284 , ARG A:288 , HOH A:905 , HOH A:974	BINDING SITE FOR RESIDUE EDO A 510
12	BC3	SOFTWARE	LEU A:127 , HIS A:297 , PHE A:299	BINDING SITE FOR RESIDUE EDO A 511
13	BC4	SOFTWARE	GLN A:184 , GLN A:186 , GLN A:283 , HOH A:621 , HOH A:765 , HOH A:813	BINDING SITE FOR RESIDUE EDO A 512
14	BC5	SOFTWARE	GLU A:291 , PHE A:292 , HOH A:692 , HOH A:723	BINDING SITE FOR RESIDUE EDO A 513

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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:307
 aligned with AKRC8_ARATH | O80944 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:307
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       
          AKRC8_ARATH     5 IRFFELNTGAKLPCVGLGTYAMVATAIEQAIKIGYRHIDCASIYGNEKEIGGVLKKLIGDGFVKREELFITSKLWSNDHLPEDVPKALEKTLQDLQIDYVDLYLIHWPASLKKESLMPTPEMLTKPDITSTWKAMEALYDSGKARAIGVSNFSSKKLTDLLNVARVTPAVNQVECHPVWQQQGLHELCKSKGVHLSGYSPLGSQSKGEVRLKVLQNPIVTEVAEKLGKTTAQVALRWGLQTGHSVLPKSSSGARLKENLDVFDWSIPEDLFTKFSNIPQEKFCRATEFAHETHGFYKTIEELWDGEI 311
               SCOP domains d3h7ra_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3h7rA00 A:5-311 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.....eee..eee....hhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhh..hhhhhhhhhhhhhhh.....eeee....ee.......hhh.ee..hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh.....eeeee......hhhhhhhhhhhh.eeeee...........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhh.......hhhhhhhhhhh.......hhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------ALDOKETO_REDUCTASE-----------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h7r A   5 IRFFELNTGAKLPCVGLGTYAMVATAIEQAIKIGYRHIDCASIYGNEKEIGGVLKKLIGDGFVKREELFITSKLWSNDHLPEDVPKALEKTLQDLQIDYVDLYLIHWPASLKKESLMPTPEMLTKPDITSTWKAMEALYDSGKARAIGVSNFSSKKLTDLLNVARVTPAVNQVECHPVWQQQGLHELCKSKGVHLSGYSPLGSQSKGEVRLKVLQNPIVTEVAEKLGKTTAQVALRWGLQTGHSVLPKSSSGARLKENLDVFDWSIPEDLFTKFSNIPQEKFCRATEFAHETHGFYKTIEELWDGEI 311
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304

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 (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AKRC8_ARATH | O80944)

molecular function
	GO:0070401	NADP+ binding	Interacting selectively and non-covalently with the oxidized form, NADP+, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
	GO:0004033	aldo-keto reductase (NADP) activity	Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + 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:0016229	steroid dehydrogenase activity	Catalysis of an oxidation-reduction (redox) reaction in which one substrate is a sterol derivative.
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:0046686	response to cadmium ion	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 a cadmium (Cd) ion stimulus.
	GO:0009409	response to cold	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 a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
	GO:0009651	response to salt 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 a stimulus indicating an increase or decrease in the concentration of salt (particularly but not exclusively sodium and chloride ions) in the environment.
	GO:0009636	response to toxic substance	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 a toxic stimulus.
	GO:0009414	response to water deprivation	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 a water deprivation stimulus, prolonged deprivation of water.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h7r)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3h7r
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	AKRC8_ARATH \| O80944
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description