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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PHAB FROM RALSTONIA EUTROPHA IN COMPLEX WITH ACETOACETYL-COA AND NADP

Authors :   K. Ikeda, Y. Tanaka, I. Tanaka, M. Yao

Date :   15 Oct 12 (Deposition) - 28 Aug 13 (Release) - 18 Dec 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Alpha/Beta Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Matsumoto, Y. Tanaka, T. Watanabe, R. Motohashi, K. Ikeda, K. Tobitani, M. Yao, I. Tanaka, S. Taguchi
Directed Evolution And Structural Analysis Of Nadph-Dependent Acetoacetyl Coenzyme A (Acetoacetyl-Coa) Reductase From Ralstonia Eutropha Reveals Two Mutations Responsible For Enhanced Kinetics
Appl. Environ. Microbiol. V. 79 6134 2013
PubMed-ID: 23913421 | Reference-DOI: 10.1128/AEM.01768-13

Molecule 1 - ACETOACETYL-COA REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.36
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PHBB, H16_A1439
	Organism Common	:	RALSTONIA EUTROPHA
	Organism Scientific	:	CUPRIAVIDUS NECATOR
	Organism Taxid	:	381666
	Strain	:	ATCC 17699 / H16 / DSM 428 / STANIER 337

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	CAA	4	Ligand/Ion	ACETOACETYL-COENZYME A
2	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:14 , THR A:188 , ASP A:189 , MET A:190 , HOH A:511 , HOH A:512 , HOH A:520 , HOH A:529 , HOH A:544	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	GLY A:10 , CYS A:34 , GLY A:35 , ARG A:40 , GLY A:60 , ASN A:61 , VAL A:62 , ALA A:89 , GLY A:90 , ILE A:91 , THR A:92 , PRO A:183 , GLY A:184 , ILE A:186 , THR A:188 , MET A:190 , VAL A:191 , CAA A:303 , HOH A:424 , HOH A:458 , HOH A:471 , HOH A:507 , HOH A:509 , HOH A:511 , HOH A:512 , HOH A:515 , HOH A:519 , HOH A:524 , HOH A:532 , HOH A:544 , HOH A:575	BINDING SITE FOR RESIDUE NAP A 302
03	AC3	SOFTWARE	THR A:92 , ASP A:94 , SER A:140 , ASN A:142 , GLN A:147 , PHE A:148 , GLY A:149 , GLN A:150 , TYR A:153 , GLY A:184 , TYR A:185 , ARG A:195 , VAL A:198 , LYS A:201 , ILE A:202 , NAP A:302 , HOH A:516 , HOH A:526 , HOH A:541 , HOH A:556 , HOH A:572	BINDING SITE FOR RESIDUE CAA A 303
04	AC4	SOFTWARE	GLY B:14 , ARG B:40 , THR B:188 , ASP B:189 , MET B:190 , NAP B:302 , HOH B:508 , HOH B:523	BINDING SITE FOR RESIDUE SO4 B 301
05	AC5	SOFTWARE	GLY B:10 , ILE B:15 , CYS B:34 , GLY B:35 , ARG B:40 , GLY B:60 , ASN B:61 , VAL B:62 , ALA B:89 , GLY B:90 , ILE B:91 , THR B:92 , THR B:111 , SER B:139 , PRO B:183 , GLY B:184 , ILE B:186 , THR B:188 , MET B:190 , VAL B:191 , SO4 B:301 , CAA B:303 , HOH B:435 , HOH B:449 , HOH B:506 , HOH B:507 , HOH B:508 , HOH B:518 , HOH B:533 , HOH B:551 , HOH B:556	BINDING SITE FOR RESIDUE NAP B 302
06	AC6	SOFTWARE	THR B:92 , ASP B:94 , GLN B:147 , PHE B:148 , GLY B:149 , GLN B:150 , TYR B:153 , GLY B:184 , TYR B:185 , ARG B:195 , VAL B:198 , NAP B:302 , HOH B:506 , HOH B:513 , HOH B:517 , HOH B:527 , HOH B:555	BINDING SITE FOR RESIDUE CAA B 303
07	AC7	SOFTWARE	GLY C:13 , GLY C:14 , THR C:188 , ASP C:189 , MET C:190 , HOH C:504	BINDING SITE FOR RESIDUE SO4 C 301
08	AC8	SOFTWARE	GLY C:10 , ILE C:15 , GLY C:35 , ARG C:40 , GLY C:60 , ASN C:61 , VAL C:62 , ALA C:89 , GLY C:90 , ILE C:91 , THR C:92 , THR C:111 , SER C:139 , PRO C:183 , GLY C:184 , ILE C:186 , THR C:188 , MET C:190 , VAL C:191 , CAA C:303 , HOH C:440 , HOH C:499 , HOH C:540	BINDING SITE FOR RESIDUE NAP C 302
09	AC9	SOFTWARE	THR C:92 , ASP C:94 , SER C:140 , ASN C:142 , GLN C:147 , PHE C:148 , GLN C:150 , TYR C:153 , GLY C:184 , TYR C:185 , ARG C:195 , NAP C:302 , HOH C:521 , HOH C:525	BINDING SITE FOR RESIDUE CAA C 303
10	BC1	SOFTWARE	GLY D:13 , GLY D:14 , THR D:188 , ASP D:189 , MET D:190 , NAP D:302	BINDING SITE FOR RESIDUE SO4 D 301
11	BC2	SOFTWARE	GLY D:10 , ILE D:15 , CYS D:34 , GLY D:35 , ARG D:40 , GLY D:60 , ASN D:61 , VAL D:62 , ALA D:89 , GLY D:90 , ILE D:91 , THR D:92 , PRO D:183 , GLY D:184 , ILE D:186 , THR D:188 , MET D:190 , VAL D:191 , SO4 D:301 , CAA D:303 , HOH D:496 , HOH D:501 , HOH D:516	BINDING SITE FOR RESIDUE NAP D 302
12	BC3	SOFTWARE	THR D:92 , ASP D:94 , SER D:140 , GLN D:147 , PHE D:148 , GLN D:150 , TYR D:153 , GLY D:184 , TYR D:185 , MET D:190 , ARG D:195 , NAP D:302 , HOH D:510	BINDING SITE FOR RESIDUE CAA D 303

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

Asymmetric/Biological Unit

No.	Residues
1	Leu D:51	-	Gly D:52

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

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	PHAB_CUPNH	140-168	4	A:140-168 B:140-168 C:140-168 D:140-168

(no "Exon" information available for 3VZS)

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:244
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
           PHAB_CUPNH     3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzsa_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzs A   3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:249
                               1                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
           PHAB_CUPNH     - ---MTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzsb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee....hhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzs B  -2 HHGSTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

Chain C from PDB  Type:PROTEIN  Length:244
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:244
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242    
           PHAB_CUPNH     3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzsc_ C: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzs C   3 QRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain D from PDB  Type:PROTEIN  Length:249
 aligned with PHAB_CUPNH | P14697 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:249
                               1                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
           PHAB_CUPNH     - ---MTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
               SCOP domains d3vzsd_ D: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh.....eeee....hhhhhhhhhhhhhhhh....eeee.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.eeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:140-168    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vzs D  -2 HHGSTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKALGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKMTRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQTNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLDKIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG 246
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Cupriavidus necator [TaxId: 381666] (4)

1a	d3vzsa_	A:
1b	d3vzsb_	B:
1c	d3vzsc_	C:
1d	d3vzsd_	D:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PHAB_CUPNH | P14697)

molecular function
	GO:0018454	acetoacetyl-CoA reductase activity	Catalysis of the reaction: (R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + 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.
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:0042619	poly-hydroxybutyrate biosynthetic process	The chemical reactions and pathways resulting in the formation of poly-hydroxybutyrate (PHB), a polymer of beta-hydroxybutyrate and a common storage material of prokaryotic cells.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Leu D:51 - Gly D:52	[ RasMol ]

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	3vzs
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	PHAB_CUPNH \| P14697
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	1.1.1.36
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		Domain Information	:	XDom
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	PHAB_CUPNH \| P14697
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UniProtKB/Swiss-Prot
	PHAB_CUPNH \| P14697	:	3vzp 3vzq 3vzr 4n5l 4n5m 4n5n

3vzp	APO FORM OF THIS ENZYME
3vzq	MUTANT OF THIS ENZYME
3vzr	ANOTHER MUTANT OF THIS ENZYME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Pfam Domains (0, 0)

Gene Ontology (5, 5)

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