1MZJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE PRIMING BETA-KETOSYNTHASE FROM THE R1128 POLYKETIDE BIOSYNTHETIC PATHWAY

Authors :   H. Pan, S. C. Tsai, E. S. Meadows, L. J. W. Miercke, A. Keatinge-Clay, J. O'Connell, C. Khosla, R. M. Stroud

Date :   08 Oct 02 (Deposition) - 11 Dec 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Beta-Ketosynthase, Aromatic Polyketide, Biosynthetic Engineering, Catalytic Triad, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Pan, S. Tsai, E. S. Meadows, L. J. Miercke, A. T. Keatinge-Clay, J. O'Connell, C. Khosla, R. M. Stroud
Crystal Structure Of The Priming Beta-Ketosynthase From The R1128 Polyketide Biosynthetic Pathway
Structure V. 10 1559
PubMed-ID: 12429097 | Reference-DOI: 10.1016/S0969-2126(02)00889-4
(for further references see the PDB file header)

Molecule 1 - BETA-KETOACYLSYNTHASE III
	Chains	:	A, B
	EC Number	:	2.3.1.41
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ZHUH
	Organism Scientific	:	STREPTOMYCES SP. R1128
	Organism Taxid	:	140437
	Synonym	:	BETA-KETOSYNTHASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	COA	2	Ligand/Ion	COENZYME A

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:37 , TRP A:41 , ARG A:45 , CYS A:121 , ARG A:160 , PHE A:164 , LEU A:165 , PHE A:166 , LEU A:198 , MET A:220 , GLY A:222 , LYS A:223 , PHE A:226 , ALA A:259 , ASN A:260 , GLU A:275 , ASN A:288 , ACE A:502 , HOH A:658 , HOH A:683 , HOH A:688	BINDING SITE FOR RESIDUE COA A 500
2	AC2	SOFTWARE	ASP B:36 , SER B:37 , TRP B:41 , ARG B:45 , CYS B:121 , ARG B:160 , PHE B:164 , PHE B:166 , MET B:220 , GLY B:222 , HIS B:257 , ALA B:259 , ASN B:260 , ASN B:288 , ACE B:503 , HOH B:543 , HOH B:633	BINDING SITE FOR RESIDUE COA B 501
3	AC3	SOFTWARE	ALA A:120 , CYS A:121 , ALA A:320 , COA A:500	BINDING SITE FOR RESIDUE ACE A 502
4	AC4	SOFTWARE	ALA B:120 , CYS B:121 , GLY B:319 , ALA B:320 , COA B:501	BINDING SITE FOR RESIDUE ACE B 503

(no "SS Bond" information available for 1MZJ)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:96	-	Pro A:97
2	Pro A:211	-	Ser A:212
3	Ala A:320	-	Gly A:321
4	Gly A:321	-	Leu A:322
5	Thr B:96	-	Pro B:97

(no "SAP(SNP)/Variant" information available for 1MZJ)

(no "PROSITE Motif" information available for 1MZJ)

(no "Exon" information available for 1MZJ)

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:334
 aligned with FABH_STRLI | Q9F6D4 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:334
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332    
           FABH_STRLI     3 GLRVPERRFSRVLGVGSYRPRREVSNKEVCTWIDSTEEWIETRTGIRSRRIAEPDETIQVMGVAASRRALEHAGVDPAEIDLVVVSTMTNFVHTPPLSVAIAHELGADNAGGFDLSAACAGFCHALSIAADAVESGGSRHVLVVATERMTDVIDLADRSLSFLFGDGAGAAVVGPSDVPGIGPVVRGIDGTGLGSLHMSSSWDQYVEDPSVGRPALVMDGKRVFRWAVADVVPAAREALEVAGLTVGDLVAFVPHQANLRIIDVLVDRLGVPEHVVVSRDAEDTGNTSSASVALALDRLVRSGAVPGGGPALMIGFGAGLSYAGQALLLPDPPS 336
               SCOP domains d1mzja1 A:3-183 Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway                                                                                             d1mzja2 A:184-336 Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway                                                                SCOP domains
               CATH domains 1mzjA01 A:3-173  [code=3.40.47.10, no name defined]                                                                                                                        1mzjA02 A:174-336  [code=3.40.47.10, no name defined]                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee....eeehhhhh.....hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeee.hhhh............eeeeeeeeeee........eeee.hhhhh.eee..hhhhhh.........eeehhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeee...hhhhhhhhhhhhh.....ee..hhhhhh...hhhhhhhhhhhhhhh......eeeeeeee...eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzj A   3 GLRVPERRFSRVLGVGSYRPRREVSNKEVCTWIDSTEEWIETRTGIRSRRIAEPDETIQVMGVAASRRALEHAGVDPAEIDLVVVSTMTNFVHTPPLSVAIAHELGADNAGGFDLSAACAGFCHALSIAADAVESGGSRHVLVVATERMTDVIDLADRSLSFLFGDGAGAAVVGPSDVPGIGPVVRGIDGTGLGSLHMSSSWDQYVEDPSVGRPALVMDGKRVFRWAVADVVPAAREALEVAGLTVGDLVAFVPHQANLRIIDVLVDRLGVPEHVVVSRDAEDTGNTSSASVALALDRLVRSGAVPGGGPALMIGFGAGLSYAGQALLLPDPPS 336
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332

Chain B from PDB  Type:PROTEIN  Length:334
 aligned with FABH_STRLI | Q9F6D4 from UniProtKB/Swiss-Prot  Length:339

    Alignment length:334
                                    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       311       321       331    
           FABH_STRLI     2 PGLRVPERRFSRVLGVGSYRPRREVSNKEVCTWIDSTEEWIETRTGIRSRRIAEPDETIQVMGVAASRRALEHAGVDPAEIDLVVVSTMTNFVHTPPLSVAIAHELGADNAGGFDLSAACAGFCHALSIAADAVESGGSRHVLVVATERMTDVIDLADRSLSFLFGDGAGAAVVGPSDVPGIGPVVRGIDGTGLGSLHMSSSWDQYVEDPSVGRPALVMDGKRVFRWAVADVVPAAREALEVAGLTVGDLVAFVPHQANLRIIDVLVDRLGVPEHVVVSRDAEDTGNTSSASVALALDRLVRSGAVPGGGPALMIGFGAGLSYAGQALLLPDPP 335
               SCOP domains d1mzjb1 B:2-183 Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway                                                                                              d1mzjb2 B:184-335 Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway                                                               SCOP domains
               CATH domains 1mzjB01 B:2-173  [code=3.40.47.10, no name defined]                                                                                                                         1mzjB02 B:174-335  [code=3.40.47.10, no name defined]                                                                                                              CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------ACP_syn_III-1mzjB01 B:115-192                                                 ------------------------------------------------ACP_syn_III_C-1mzjB03 B:241-331                                                            ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------ACP_syn_III-1mzjB02 B:115-192                                                 ------------------------------------------------ACP_syn_III_C-1mzjB04 B:241-331                                                            ---- Pfam domains (2)
         Sec.struct. author .........eeeeeeeeee....eeehhhhh.......hhhhhh....eee......hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhh.....eeeeeeee.hhhh............eeeeeeeeeee........eeee.hhhh..eee..hhhhhh.........eeehhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.eeee...hhhhhhhhhhhhh.....ee..hhhhhh...hhhhhhhhhhhhh........eeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzj B   2 PGLRVPERRFSRVLGVGSYRPRREVSNKEVCTWIDSTEEWIETRTGIRSRRIAEPDETIQVMGVAASRRALEHAGVDPAEIDLVVVSTMTNFVHTPPLSVAIAHELGADNAGGFDLSAACAGFCHALSIAADAVESGGSRHVLVVATERMTDVIDLADRSLSFLFGDGAGAAVVGPSDVPGIGPVVRGIDGTGLGSLHMSSSWDQYVEDPSVGRPALVMDGKRVFRWAVADVVPAAREALEVAGLTVGDLVAFVPHQANLRIIDVLVDRLGVPEHVVVSRDAEDTGNTSSASVALALDRLVRSGAVPGGGPALMIGFGAGLSYAGQALLLPDPP 335
                                    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       311       321       331

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: Thiolase-like (231)

Superfamily: Thiolase-like (231)

Family: Chalcone synthase-like (56)

Protein domain: Priming beta-ketosynthase from the r1128 polyketide biosynthetic pathway (1)

Streptomyces sp. r1128 [TaxId: 140437] (1)

1a	d1mzja1	A:3-183
1b	d1mzja2	A:184-336
1c	d1mzjb1	B:2-183
1d	d1mzjb2	B:184-335

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Peroxisomal Thiolase; Chain A, domain 1 (130)

Homologous Superfamily: [code=3.40.47.10, no name defined] (130)

R1128 (Streptomyces sp) (1)

1a	1mzjB01	B:2-173
1b	1mzjA01	A:3-173
1c	1mzjA02	A:174-336
1d	1mzjB02	B:174-335

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Thiolase (72)

Family: ACP_syn_III (12)

Streptomyces lividans (1)

1a	ACP_syn_III-1mzjB01	B:115-192
1b	ACP_syn_III-1mzjB02	B:115-192

Family: ACP_syn_III_C (12)

Streptomyces lividans (1)

2a	ACP_syn_III_C-1mzjB03	B:241-331
2b	ACP_syn_III_C-1mzjB04	B:241-331

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FABH_STRLI | Q9F6D4)

molecular function
	GO:0004315	3-oxoacyl-[acyl-carrier-protein] synthase activity	Catalysis of the reaction: acyl-[acyl-carrier protein] + malonyl-[acyl-carrier protein] = 3-oxoacyl-[acyl-carrier protein] + CO2 + [acyl-carrier protein].
	GO:0033818	beta-ketoacyl-acyl-carrier-protein synthase III activity	Catalysis of the reaction: acetyl-CoA + malonyl-[acyl-carrier protein] = acetoacyl-[acyl-carrier protein] + CoA + CO2.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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
	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
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		COA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:320 - Gly A:321	[ RasMol ]
		Gly A:321 - Leu A:322	[ RasMol ]
		Pro A:211 - Ser A:212	[ RasMol ]
		Thr A:96 - Pro A:97	[ RasMol ]
		Thr B:96 - Pro B:97	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	1mzj
		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
	FABH_STRLI \| Q9F6D4
		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)
	2.3.1.41
		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
	FABH_STRLI \| Q9F6D4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1MZJ)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (2, 4)

Gene Ontology (10, 10)

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