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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BOMBYX MORI ALDO-KETO REDUCTASE (AKR2E4) IN COMPLEX WITH NADP

Authors :   K. Yamamoto, D. K. Wilson

Date :   05 Jun 13 (Deposition) - 01 Jan 14 (Release) - 01 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A

Keywords :   Tim-Barrel, Reductase, Nadp, Cytosol, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Yamamoto, D. K. Wilson
Identification, Characterization, And Crystal Structure Of An Aldo-Keto Reductase (Akr2E4) From The Silkworm Bombyx Mori.
Arch. Biochem. Biophys. V. 538 156 2013
PubMed-ID: 24012638 | Reference-DOI: 10.1016/J.ABB.2013.08.018

Molecule 1 - ALDO-KETO REDUCTASE 2E
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	AKR2E
	Organism Common	:	SILK MOTH,SILKWORM
	Organism Scientific	:	BOMBYX MORI
	Organism Taxid	:	7091
	Synonym	:	UNCHARACTERIZED PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	NAP	1	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:22 , THR A:23 , GLY A:24 , THR A:27 , LYS A:29 , ASP A:53 , TYR A:58 , HIS A:120 , SER A:158 , ASN A:159 , GLN A:180 , TYR A:206 , SER A:207 , PRO A:208 , PHE A:209 , VAL A:213 , ARG A:215 , ILE A:257 , PRO A:258 , LYS A:259 , SER A:260 , THR A:261 , ARG A:265 , ASN A:269 , CIT A:406 , HOH A:561 , HOH A:577 , HOH A:608 , HOH A:612 , HOH A:619 , HOH A:629 , HOH A:646 , HOH A:680 , HOH A:708	BINDING SITE FOR RESIDUE NAP A 401
2	AC2	SOFTWARE	TYR A:173 , ILE A:174 , ARG A:175 , HOH A:653	BINDING SITE FOR RESIDUE EDO A 402
3	AC3	SOFTWARE	THR A:15 , PRO A:17 , GLU A:80 , GLU A:81 , LEU A:82 , HOH A:647 , HOH A:691	BINDING SITE FOR RESIDUE EDO A 403
4	AC4	SOFTWARE	ASN A:74 , LEU A:76 , ASN A:289 , ASN A:291 , HOH A:651 , HOH A:655 , HOH A:723	BINDING SITE FOR RESIDUE EDO A 404
5	AC5	SOFTWARE	ASN A:159 , GLN A:189 , LEU A:192 , ARG A:293 , ASN A:308 , HOH A:580	BINDING SITE FOR RESIDUE EDO A 405
6	AC6	SOFTWARE	GLY A:24 , ARG A:25 , GLY A:26 , TYR A:58 , NAP A:401 , HOH A:577 , HOH A:619 , HOH A:631 , HOH A:677	BINDING SITE FOR RESIDUE CIT A 406

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:222	-	Pro A:223

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALDOKETO_REDUCTASE_1	PS00798	Aldo/keto reductase family signature 1.	AK2E4_BOMMO	48-65	1	A:48-65
2	ALDOKETO_REDUCTASE_2	PS00062	Aldo/keto reductase family signature 2.	AK2E4_BOMMO	143-160	1	A:143-160
3	ALDOKETO_REDUCTASE_3	PS00063	Aldo/keto reductase family putative active site signature.	AK2E4_BOMMO	257-272	1	A:257-272

(no "Exon" information available for 3WCZ)

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
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Chain A from PDB  Type:PROTEIN  Length:307
 aligned with AK2E4_BOMMO | H9JTG9 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:307
                                    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       
          AK2E4_BOMMO     2 AVQAPCIQLNDGNTIPIVALGTGRGTAKESDSIDEVRQAVYWAIEAGYRHIDTAAVYQDEEQVGQGIAEAIANGLVTREELFVTTKLWNDKHARDQVVPALQESLKKLGLDYIDLYLIHFPIATKPDDSPDNIDYLETWQGMQDARQLGLARSIGVSNFNATQITRLVSNSYIRPVINQIEVNPTNTQEPLVAHCQSLGIAVMAYSPFGFVVSRGQTGAPPPRSDDPTLTALANKYRKSVGQILLRYLIDRGLIPIPKSTNKQRIAQNIDLFDFQLTFEEVAAINQFNKNHRVIDISDWKDYPNYPN 308
               SCOP domains d3wcza_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.....eee...ee...........hhhhhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeee.....hhhhhhhhhhhhhhhhh...eeeeee....ee.....ee..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhh......eeeee......hhhhhhhhhhh..eeeee..hhhhh.............hhhhhhhhhhhh.hhhhhhhhhhhhh..ee.....hhhhhhhhhh......hhhhhhhhhh.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------ALDOKETO_REDUCTASE-----------------------------------------------------------------------------ALDOKETO_REDUCTASE------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wcz A   2 AVQAPCIQLNDGNTIPIVALGTGRGTAKESDSIDEVRQAVYWAIEAGYRHIDTAAVYQDEEQVGQGIAEAIANGLVTREELFVTTKLWNDKHARDQVVPALQESLKKLGLDYIDLYLIHFPIATKPDDSPDNIDYLETWQGMQDARQLGLARSIGVSNFNATQITRLVSNSYIRPVINQIEVNPTNTQEPLVAHCQSLGIAVMAYSPFGFVVSRGQTGAPPPRSDDPTLTALANKYRKSVGQILLRYLIDRGLIPIPKSTNKQRIAQNIDLFDFQLTFEEVAAINQFNKNHRVIDISDWKDYPNYPN 308
                                    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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: NAD(P)-linked oxidoreductase (286)

Family: automated matches (35)

Protein domain: automated matches (35)

Silkworm (Bombyx mori) [TaxId: 7091] (1)

d3wcza_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AK2E4_BOMMO | H9JTG9)

molecular function
	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.
biological process
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		CIT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Pro A:222 - Pro A:223	[ RasMol ]

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	3wcz
		Family and Domain Information	:	ProDom \| SYSTERS
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	AK2E4_BOMMO \| H9JTG9
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (4, 4)

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