3RI3 - JenaLib

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Title :   ACTINORHODIN POLYKETIDE KETOREDUCTASE MUTANT P94L BOUND TO NADPH AND THE INHIBITOR EMODIN

Authors :   P. Javidpour, S. -C. Tsai

Date :   12 Apr 11 (Deposition) - 29 Jun 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.29

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

Keywords :   Actinorhodin, Polyketide, Ketoreductase, Short-Chain Dehydrogenase/Reductase, Rossmann Fold, Type Ii Polyketide Ketoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Javidpour, T. P. Korman, G. Shakya, S. C. Tsai
Structural And Biochemical Analyses Of Regio- And Stereospecificities Observed In A Type Ii Polyketide Ketoreductase.
Biochemistry V. 50 4638 2011
PubMed-ID: 21506596 | Reference-DOI: 10.1021/BI200335F

Molecule 1 - KETOACYL REDUCTASE
	Chains	:	B, A
	EC Number	:	1.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ACTIII, SCBAC28G1.12C, SCO5086
	Organism Scientific	:	STREPTOMYCES COELICOLOR
	Organism Taxid	:	1902

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	EMO	4	Ligand/Ion	3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
2	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	EMO	8	Ligand/Ion	3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
2	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:13 , THR B:15 , SER B:16 , ILE B:18 , ARG B:38 , GLY B:39 , CYS B:62 , ASP B:63 , VAL B:64 , ASN B:90 , ALA B:91 , ILE B:142 , ALA B:143 , SER B:144 , TYR B:157 , LYS B:161 , PRO B:187 , GLY B:188 , VAL B:190 , THR B:192 , PRO B:193 , MET B:194 , HOH B:296 , EMO B:303	BINDING SITE FOR RESIDUE NDP B 301
2	AC2	SOFTWARE	SER B:144 , THR B:145 , GLN B:149 , TYR B:157 , VAL B:198 , LEU B:258 , EMO B:303	BINDING SITE FOR RESIDUE EMO B 302
3	AC3	SOFTWARE	SER B:144 , TYR B:157 , GLY B:188 , PHE B:189 , MET B:194 , VAL B:198 , ILE B:217 , LEU B:258 , NDP B:301 , EMO B:302	BINDING SITE FOR RESIDUE EMO B 303
4	AC4	SOFTWARE	GLY A:13 , THR A:15 , SER A:16 , GLY A:17 , ILE A:18 , ALA A:37 , ARG A:38 , GLY A:39 , CYS A:62 , ASP A:63 , VAL A:64 , ASN A:90 , ALA A:91 , GLY A:92 , ILE A:142 , ALA A:143 , SER A:144 , TYR A:157 , LYS A:161 , PRO A:187 , GLY A:188 , VAL A:190 , THR A:192 , PRO A:193 , MET A:194 , HOH A:264 , HOH A:265 , HOH A:297 , EMO A:302 , HOH A:309 , HOH A:312 , ARG B:51 , HOH B:290	BINDING SITE FOR RESIDUE NDP A 301
5	AC5	SOFTWARE	LEU A:94 , SER A:144 , THR A:145 , TYR A:157 , GLY A:188 , PHE A:189 , VAL A:198 , ILE A:217 , NDP A:301 , EMO A:303	BINDING SITE FOR RESIDUE EMO A 302
6	AC6	SOFTWARE	LEU A:94 , SER A:144 , THR A:145 , GLY A:146 , GLN A:149 , VAL A:151 , EMO A:302	BINDING SITE FOR RESIDUE EMO A 303

(no "SS Bond" information available for 3RI3)

Asymmetric Unit

No.	Residues
1	Arg B:-3	-	Gly B:-2
2	Glu B:200	-	His B:201

(no "SAP(SNP)/Variant" information available for 3RI3)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	ACT3_STRCO	144-172	2	A:144-172 B:144-172

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	ACT3_STRCO	144-172	4	A:144-172 B:144-172

(no "Exon" information available for 3RI3)

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:256
 aligned with ACT3_STRCO | P16544 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:256
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255      
           ACT3_STRCO     6 SEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
               SCOP domains d3ri3a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhh..hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:144-172    ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ri3 A   6 SEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRLGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain B from PDB  Type:PROTEIN  Length:257
 aligned with ACT3_STRCO | P16544 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:265
                                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     
           ACT3_STRCO     - ----MATQDSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
               SCOP domains d3ri3b_ B: automated matches                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------adh_short-3ri3B01 B:7-176                                                                                                                                                 ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------adh_short-3ri3B02 B:7-176                                                                                                                                                 ------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...........eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhh..--------..hhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:144-172    ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ri3 B  -3 RGSHMATQDSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRLGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREH--------TEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196    |    -   |   216       226       236       246       256     
                                                                                                                                                                                                                                      201      210

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: automated matches (114)

Streptomyces coelicolor [TaxId: 1902] (5)

1a	d3ri3a_	A:
1b	d3ri3b_	B:

(no "CATH Domain" information available for 3RI3)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Streptomyces coelicolor (7)

1a	adh_short-3ri3B01	B:7-176
1b	adh_short-3ri3B02	B:7-176

Asymmetric Unit(hide GO term definitions)

Chain A,B (ACT3_STRCO | P16544)

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:0017000	antibiotic biosynthetic process	The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	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
		Arg B:-3 - Gly B:-2	[ RasMol ]
		Glu B:200 - His B:201	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	3ri3
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	ACT3_STRCO \| P16544	:	1w4z 1x7g 1x7h 1xr3 2rh4 2rhc 2rhr 3csd 3qrw 4dbz 4dc0 4dc1

(no "Related Entries Specified in the PDB File" available for 3RI3)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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