2RHC - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACTINORHODIN KETORDEUCTASE, ACTKR, WITH NADP+ AND INHIBITOR EMODIN

Authors :   T. P. Korman, S. -C. Tsai

Date :   08 Oct 07 (Deposition) - 19 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Oxidoreductase, Polyketide, Actinorhodin, Ketoreductase, Combinatorial Biosynthesis, Short Chain Dehydrogenase/Reductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. P. Korman, Y. H. Tan, J. Wong, R. Luo, S. -C. Tsai
Inhibition Kinetics And Emodin Cocrystal Structure Of A Type Ii Polyketide Ketoreductase
Biochemistry V. 47 1837 2008
PubMed-ID: 18205400 | Reference-DOI: 10.1021/BI7016427
(for further references see the PDB file header)

Molecule 1 - ACTINORHODIN POLYKETIDE KETOREDUCTASE
	Chains	:	B, A
	EC Number	:	1.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PYT284
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PET28B(+)
	Gene	:	ACTIII
	Organism Scientific	:	STREPTOMYCES COELICOLOR
	Synonym	:	KETOACYL REDUCTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	EMO	1	Ligand/Ion	3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
2	NAP	2	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	EMO	2	Ligand/Ion	3-METHYL-1,6,8-TRIHYDROXYANTHRAQUINONE
2	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:13 , THR B:15 , SER B:16 , GLY B:17 , ILE B:18 , ARG B:38 , GLY B:39 , CYS B:62 , ASP B:63 , ASN B:90 , GLY B:92 , ILE B:142 , ALA B:143 , SER B:144 , TYR B:157 , LYS B:161 , PRO B:187 , GLY B:188 , THR B:192 , PRO B:193 , MET B:194 , HOH B:310 , HOH B:329 , HOH B:357	BINDING SITE FOR RESIDUE NAP B 301
2	AC2	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 , ASN A:90 , GLY A:92 , ILE A:142 , ALA A:143 , SER A:144 , TYR A:157 , LYS A:161 , PRO A:187 , GLY A:188 , THR A:192 , PRO A:193 , HOH A:405 , HOH A:411 , HOH A:419 , HOH A:469 , ARG B:51	BINDING SITE FOR RESIDUE NAP A 301
3	AC3	SOFTWARE	SER A:144 , THR A:145 , GLY A:146 , GLN A:149 , TYR A:157 , PHE A:189	BINDING SITE FOR RESIDUE EMO A 401

(no "SS Bond" information available for 2RHC)

(no "Cis Peptide Bond" information available for 2RHC)

(no "SAP(SNP)/Variant" information available for 2RHC)

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 2RHC)

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:257
 aligned with ACT3_STRCO | P16544 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:257
                                    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       
           ACT3_STRCO     5 DSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
               SCOP domains d2rhca_ A: beta-keto acyl carrier protein reductase                                                                                                                                                                                                               SCOP domains
               CATH domains 2rhcA00 A:5-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..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
                 2rhc A   5 DSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
                                    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

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with ACT3_STRCO | P16544 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:268
                                   1                                                                                                                                                                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253        
           ACT3_STRCO     - -------MATQDSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
               SCOP domains d2rhcb_ B: beta-keto acyl carrier protein reductase                                                                                                                                                                                                                          SCOP domains
               CATH domains 2rhcB00 B:-6-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) -------------adh_short-2rhcB01 B:7-176                                                                                                                                                 ------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------adh_short-2rhcB02 B:7-176                                                                                                                                                 ------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ..............eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhheeeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:144-172    ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rhc B  -6 LVPRGSHMATQDSEVALVTGATSGIGLEIARRLGKEGLRVFVCARGEEGLRTTLKELREAGVEADGRTCDVRSVPEIEALVAAVVERYGPVDVLVNNAGRPGGGATAELADELWLDVVETNLTGVFRVTKQVLKAGGMLERGTGRIVNIASTGGKQGVVHAAPYSASKHGVVGFTKALGLELARTGITVNAVCPGFVETPMAASVREHYSDIWEVSTEEAFDRITARVPIGRYVQPSEVAEMVAYLIGPGAAAVTAQALNVCGGLGNY 261
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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: beta-keto acyl carrier protein reductase (19)

Streptomyces coelicolor [TaxId: 1902] (8)

1a	d2rhca_	A:
1b	d2rhcb_	B:

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)

Streptomyces coelicolor. (3)

1a	2rhcA00	A:5-261
1b	2rhcB00	B:-6-261

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Streptomyces coelicolor (7)

1a	adh_short-2rhcB01	B:7-176
1b	adh_short-2rhcB02	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.

Asymmetric 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
		EMO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rhc)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2rhc
		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
	ACT3_STRCO \| P16544
		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)
	1.3.1.-
		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

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ACT3_STRCO \| P16544
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ACT3_STRCO \| P16544	:	1w4z 1x7g 1x7h 1xr3 2rh4 2rhr 3csd 3qrw 3ri3 4dbz 4dc0 4dc1

1x7g	ACTINORHODIN POLYKETIDE KETOREDUCTASE, WITH NADP BOUND
1x7h	ACTINORHODIN POLYKETIDE KETOREDUCTASE, WITH NADPH BOUND
2rh4
2rhr

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (3, 3)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File