2H7X - JenaLib

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Title :   PIKROMYCIN THIOESTERASE ADDUCT WITH REDUCED TRIKETIDE AFFINITY LABEL

Authors :   J. W. Giraldes, D. L. Akey, J. D. Kittendorf, D. H. Sherman, J. S. Smith, R. A. Fecik

Date :   05 Jun 06 (Deposition) - 19 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Thioesterase, Alpha-Beta Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Giraldes, D. L. Akey, J. D. Kittendorf, D. H. Sherman, J. S. Smith, R. A. Fecik
Structural And Mechanistic Insights Of Polyketide Macrolactonization From Polyketide-Based Affinity Labels
Nat. Chem. Biol. V. 2 531 2006
PubMed-ID: 16969373 | Reference-DOI: 10.1038/NCHEMBIO822
(for further references see the PDB file header)

Molecule 1 - TYPE I POLYKETIDE SYNTHASE PIKAIV
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	THIOESTERASE DOMAIN
	Gene	:	PIKAIV
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571
	Synonym	:	PIKROMYCIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	PSX	2	Ligand/Ion	[(2S,3R,4S)-2,4-DIHYDROXY-3-METHYLHEXYL]PHOSPHONICACID
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PSX	2	Ligand/Ion	[(2S,3R,4S)-2,4-DIHYDROXY-3-METHYLHEXYL]PHOSPHONICACID
4	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 14)

No.	Name	Count	Type	Full Name
1	DMS	4	Ligand/Ion	DIMETHYL SULFOXIDE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	PSX	4	Ligand/Ion	[(2S,3R,4S)-2,4-DIHYDROXY-3-METHYLHEXYL]PHOSPHONICACID
4	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:24 , ALA B:37 , GLN B:41 , ARG B:215 , HOH B:615	BINDING SITE FOR RESIDUE SO4 B 503
2	AC2	SOFTWARE	ALA A:37 , GLN A:41 , ARG A:215 , HOH A:733 , HOH A:773 , ARG B:24	BINDING SITE FOR RESIDUE SO4 A 504
3	AC3	SOFTWARE	HIS A:254 , ASP A:256 , HOH A:581	BINDING SITE FOR RESIDUE MG A 507
4	AC4	SOFTWARE	ARG A:248 , GLN B:245 , GLU B:246 , GLU B:247	BINDING SITE FOR RESIDUE SO4 A 505
5	AC5	SOFTWARE	SER A:148 , GLY A:149 , ILE A:186 , ALA A:217 , LEU A:220 , HIS A:268 , HOH A:549 , HOH A:550 , HOH A:553 , HOH A:743 , HOH A:783	BINDING SITE FOR RESIDUE PSX A 548
6	AC6	SOFTWARE	SER B:148 , GLY B:149 , LEU B:152 , ILE B:186 , LEU B:220 , HIS B:268 , HOH B:571 , HOH B:644 , HOH B:762 , HOH B:783	BINDING SITE FOR RESIDUE PSX B 548
7	AC7	SOFTWARE	ARG B:227 , TRP B:255 , ASP B:256	BINDING SITE FOR RESIDUE DMS B 501
8	AC8	SOFTWARE	GLN A:192 , GLY A:242 , ASP A:243 , HOH A:683	BINDING SITE FOR RESIDUE DMS B 502

(no "SS Bond" information available for 2H7X)

(no "Cis Peptide Bond" information available for 2H7X)

(no "SAP(SNP)/Variant" information available for 2H7X)

(no "PROSITE Motif" information available for 2H7X)

(no "Exon" information available for 2H7X)

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
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Chain A from PDB  Type:PROTEIN  Length:279
 aligned with PIKA4_STRVZ | Q9ZGI2 from UniProtKB/Swiss-Prot  Length:1346

    Alignment length:284
                                  1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336    
         PIKA4_STRVZ   1057 AGMFRALFRQAVEDDRYGEFLDVLAEASAFRPQFASPEACSERLDPVLLAGGPTDRAEGRAVLVGCTGTAANGGPHEFLRLSTSFQEERDFLAVPLPGYGTGTGTGTALLPADLDTALDAQARAILRAAGDAPVVLLGHSGGALLAHELAFRLERAHGAPPAGIVLVDPYPPGHQEPIEVWSRQLGEGLFAGELEPMSDARLLAMGRYARFLAGPRPGRSSAPVLLVRASEPLGDWQEERGDWRAHWDLPHTVADVPGDHFTMMRDHAPAVAEAVLSWLDAIEG 1340
               SCOP domains d2h7xa_ A: Picromycin polyketide synthase                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2h7xA00 A:9-292  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhh...ee.hhhhh......eeee.....--....eeeee...........hhhhhhh......eeee........---....ee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.......hhhhh..........eeeee....hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h7x A    9 AGMFRALFRQAVEDDRYGEFLDVLAEASAFRPQFASPEACSERLDPVLLAGGPTD--EGRAVLVGCTGTAANGGPHEFLRLSTSFQEERDFLAVPLPGYGTG---GTALLPADLDTALDAQARAILRAAGDAPVVLLGHSGGALLAHELAFRLERAHGAPPAGIVLVDPYPPGHQEPIEVWSRQLGEGLFAGELEPMSDARLLAMGRYARFLAGPRPGRSSAPVLLVRASEPLGDWQEERGDWRAHWDLPHTVADVPGDHFTMMRDHAPAVAEAVLSWLDAIEG  292
                                    18        28        38        48        58    |  |68        78        88        98       108 |   | 118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288    
                                                                                 63 66                                         110 114

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with PIKA4_STRVZ | Q9ZGI2 from UniProtKB/Swiss-Prot  Length:1346

    Alignment length:283
                                  1066      1076      1086      1096      1106      1116      1126      1136      1146      1156      1166      1176      1186      1196      1206      1216      1226      1236      1246      1256      1266      1276      1286      1296      1306      1316      1326      1336   
         PIKA4_STRVZ   1057 AGMFRALFRQAVEDDRYGEFLDVLAEASAFRPQFASPEACSERLDPVLLAGGPTDRAEGRAVLVGCTGTAANGGPHEFLRLSTSFQEERDFLAVPLPGYGTGTGTGTALLPADLDTALDAQARAILRAAGDAPVVLLGHSGGALLAHELAFRLERAHGAPPAGIVLVDPYPPGHQEPIEVWSRQLGEGLFAGELEPMSDARLLAMGRYARFLAGPRPGRSSAPVLLVRASEPLGDWQEERGDWRAHWDLPHTVADVPGDHFTMMRDHAPAVAEAVLSWLDAIE 1339
               SCOP domains d2h7xb_ B: Picromycin polyketide synthase                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2h7xB00 B:9-291  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhh...ee.hhhhh......eeee.....--....eeeee...........hhhhhhh......eeee......-----....ee.hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.........eeeeee.......hhhhh..........eeeee....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2h7x B    9 AGMFRALFRQAVEDDRYGEFLDVLAEASAFRPQFASPEACSERLDPVLLAGGPTD--EGRAVLVGCTGTAANGGPHEFLRLSTSFQEERDFLAVPLPGYG-----GTALLPADLDTALDAQARAILRAAGDAPVVLLGHSGGALLAHELAFRLERAHGAPPAGIVLVDPYPPGHQEPIEVWSRQLGEGLFAGELEPMSDARLLAMGRYARFLAGPRPGRSSAPVLLVRASEPLGDWQEERGDWRAHWDLPHTVADVPGDHFTMMRDHAPAVAEAVLSWLDAIE  291
                                    18        28        38        48        58    |  |68        78        88        98       108     | 118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288   
                                                                                 63 66                                       108   114

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: alpha/beta-Hydrolases (971)

Superfamily: alpha/beta-Hydrolases (971)

Family: Thioesterase domain of polypeptide, polyketide and fatty acid synthases (11)

Protein domain: Picromycin polyketide synthase (7)

Streptomyces venezuelae [TaxId: 54571] (7)

1a	d2h7xa_	A:
1b	d2h7xb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1820, no name defined] (692)

Streptomyces venezuelae. Organism_taxid: 54571. (7)

1a	2h7xA00	A:9-292
1b	2h7xB00	B:9-291

(no "Pfam Domain" information available for 2H7X)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PIKA4_STRVZ | Q9ZGI2)

molecular function
	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:0016788	hydrolase activity, acting on ester bonds	Catalysis of the hydrolysis of any ester bond.
	GO:0031177	phosphopantetheine binding	Interacting selectively and non-covalently with phosphopantetheine, the vitamin pantetheine 4'-(dihydrogen phosphate).
	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:0016747	transferase activity, transferring acyl groups other than amino-acyl groups	Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0033068	macrolide biosynthetic process	The chemical reactions and pathways leading to the formation of macrolides, any of a large group of polyketide compounds that contain a large lactone ring with few or no double bonds and no nitrogen atoms, linked glycosidically to one or more sugar groups. The macrolides include the carbomycins, the erythromycins, oleandomycin, oligomycins, and the spiramycins, and act as antibiotics, mainly against Gram-positive bacteria.
	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.

Asymmetric Unit
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	2h7x
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	PIKA4_STRVZ \| Q9ZGI2
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UniProtKB/Swiss-Prot
	PIKA4_STRVZ \| Q9ZGI2	:	1mn6 1mna 1mnq 2h7y 2hfj 2hfk 3f5h

1mna	PIKROMYCIN THIOESTERASE
2h7y	PIKROMYCIN THIOESTERASE WITH COVALENT AFFINITY LABEL

Description

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Ligands, Modified Residues, Ions (4, 8)

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