3TZY - JenaLib

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Title :   CRYSTAL STRUCTURE OF A FRAGMENT CONTAINING THE ACYLTRANSFERASE DOMAIN OF PKS13 FROM MYCOBACTERIUM TUBERCULOSIS IN THE PALMITOYLATED FORM AT 2.2 A

Authors :   F. Bergeret, J. D. Pedelacq, L. Mourey, C. Bon

Date :   28 Sep 11 (Deposition) - 29 Aug 12 (Release) - 17 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Acyltransferase, Long Fatty Acid Chain Transferase, Acyl Carrier Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Bergeret, S. Gavalda, C. Chalut, W. Malaga, A. Quemard, J. D. Pedelacq, M. Daffe, C. Guilhot, L. Mourey, C. Bon
Biochemical And Structural Study Of The Atypical Acyltransferase Domain From The Mycobacterial Polyketide Synthase Pks13
J. Biol. Chem. V. 287 33675 2012
PubMed-ID: 22825853 | Reference-DOI: 10.1074/JBC.M111.325639

Molecule 1 - POLYKETIDE SYNTHASE PKS13
	Chains	:	A, B
	EC Number	:	2.3.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PWM71, PET28AII
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ACYLTRANSFERASE DOMAIN, UNP RESIDUES 576-1062
	Gene	:	RV3800C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	POLYKETIDE SYNTHASE

Molecule 2 - 12-MER PEPTIDE
	Chains	:	C, D
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	THE AUTHOR PRESUME THAT THIS PEPTIDE COMES FROM THE ESCHERICHIA COLI STRAIN THAT WAS USED TO PRODUCE THE RECOMBINANT PROTEIN.
	Synonym	:	CO-CRYSTALLIZED PEPTIDE

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A			D
Biological Unit 2 (1x)	:		B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 11)

No.	Name	Count	Type	Full Name
1	GOL	7	Ligand/Ion	GLYCEROL
2	PLM	2	Ligand/Ion	PALMITIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	PLM	1	Ligand/Ion	PALMITIC ACID
3	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PLM	1	Ligand/Ion	PALMITIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:719 , GLN A:773 , SER A:801 , LEU A:802 , ARG A:826 , MET A:830 , GLY A:833 , GLU A:834 , THR A:904 , GLY A:906 , SER A:908 , HIS A:909 , MET A:913	BINDING SITE FOR RESIDUE PLM A 2001
02	AC2	SOFTWARE	TYR A:754 , THR A:771	BINDING SITE FOR RESIDUE GOL A 2002
03	AC3	SOFTWARE	TYR A:945 , SER A:979 , HIS A:981	BINDING SITE FOR RESIDUE GOL A 2003
04	AC4	SOFTWARE	GLY A:720 , GLN A:722 , ARG A:900 , ALA A:903	BINDING SITE FOR RESIDUE GOL A 2004
05	AC5	SOFTWARE	GLY A:711 , PRO A:712 , LYS A:793 , HIS A:1037 , ASP A:1038 , HOH A:2132	BINDING SITE FOR RESIDUE GOL A 2005
06	AC6	SOFTWARE	ASP A:681 , HIS A:682	BINDING SITE FOR RESIDUE GOL A 2006
07	AC7	SOFTWARE	PHE B:719 , SER B:801 , LEU B:802 , ARG B:826 , MET B:830 , GLY B:833 , GLU B:834 , THR B:904 , GLY B:906 , SER B:908 , HIS B:909 , GLN B:912 , MET B:913 , HOH B:2207	BINDING SITE FOR RESIDUE PLM B 2001
08	AC8	SOFTWARE	GLY B:711 , PRO B:712 , HIS B:1037 , ASP B:1038 , HOH B:2101 , HOH B:2129	BINDING SITE FOR RESIDUE GOL B 2002
09	AC9	SOFTWARE	TYR B:754 , GLU B:770 , THR B:771	BINDING SITE FOR RESIDUE GOL B 2003
10	BC1	SOFTWARE	ASN B:990 , ARG B:1017	BINDING SITE FOR RESIDUE SO4 B 2004
11	BC2	SOFTWARE	GLN B:1019 , LYS C:3 , ASN C:5 , PHE C:6	BINDING SITE FOR RESIDUE SO4 C 101

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

(no "Cis Peptide Bond" information available for 3TZY)

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

(no "PROSITE Motif" information available for 3TZY)

(no "Exon" information available for 3TZY)

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:464
 aligned with O53579_MYCTO | O53579 from UniProtKB/TrEMBL  Length:1733

    Alignment length:464
                                   605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055    
        O53579_MYCTO    596 ELPGVTEEALRLKEAALEELAAQEVTAPLVPLAVSAFLTSRKKAAAAELADWMQSPEGQASSLESIGRSLSRRNHGRSRAVVLAHDHDEAIKGLRAVAAGKQAPNVFSVDGPVTTGPVWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDAQDYGIETTQVTIFAIQIALGELLRHHGAKPAAVIGQSLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEAMLFGEYIRLMALVEYSADEIREVFSDFPDLEVCVYAAPTQTVIGGPPEQVDAILARAEAEGKFARKFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGRYIKPGGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALTTADAGLHDAQLIPTLARKQDEVSSMVSTMAQLYVYGHDLDIRTLFSRASGPQDYANIPP 1059
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhh......eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhh...eeeeeee..eeeeeehhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh..........eeee.....eee........hhhhhhhhhhh..hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhh....hhhhhh....hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3tzy A  596 ELPGVTEEALRLKEAALEELAAQEVTAPLVPLAVSAFLTSRKKAAAAELADWMQSPEGQASSLESIGRSLSRRNHGRSRAVVLAHDHDEAIKGLRAVAAGKQAPNVFSVDGPVTTGPVWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDAQDYGIETTQVTIFAIQIALGELLRHHGAKPAAVIGQSLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEAMLFGEYIRLMALVEYSADEIREVFSDFPDLEVCVYAAPTQTVIGGPPEQVDAILARAEAEGKFARKFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGRYIKPGGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALTTADAGLHDAQLIPTLARKQDEVSSMVSTMAQLYVYGHDLDIRTLFSRASGPQDYANIPP 1059
                                   605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055

Chain B from PDB  Type:PROTEIN  Length:466
 aligned with O53579_MYCTO | O53579 from UniProtKB/TrEMBL  Length:1733

    Alignment length:466
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056      
        O53579_MYCTO    597 LPGVTEEALRLKEAALEELAAQEVTAPLVPLAVSAFLTSRKKAAAAELADWMQSPEGQASSLESIGRSLSRRNHGRSRAVVLAHDHDEAIKGLRAVAAGKQAPNVFSVDGPVTTGPVWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDAQDYGIETTQVTIFAIQIALGELLRHHGAKPAAVIGQSLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEAMLFGEYIRLMALVEYSADEIREVFSDFPDLEVCVYAAPTQTVIGGPPEQVDAILARAEAEGKFARKFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGRYIKPGGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALTTADAGLHDAQLIPTLARKQDEVSSMVSTMAQLYVYGHDLDIRTLFSRASGPQDYANIPPTRF 1062
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.....eeeeeee.hhhhhhhhhhhhhh......eeee........eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...hhhhh.eeeee..hhhhhhh........eeeeeee..eeeeeehhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhh.........eeee.....eee........hhhhhhhhhhh..hhhhhhhhhhhh...eeee....hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhhhhh....hhhhhh....hhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3tzy B  597 LPGVTEEALRLKEAALEELAAQEVTAPLVPLAVSAFLTSRKKAAAAELADWMQSPEGQASSLESIGRSLSRRNHGRSRAVVLAHDHDEAIKGLRAVAAGKQAPNVFSVDGPVTTGPVWVLAGFGAQHRKMGKSLYLRNEVFAAWIEKVDALVQDELGYSVLELILDDAQDYGIETTQVTIFAIQIALGELLRHHGAKPAAVIGQSLGEAASAYFAGGLSLRDATRAICSRSHLMGEGEAMLFGEYIRLMALVEYSADEIREVFSDFPDLEVCVYAAPTQTVIGGPPEQVDAILARAEAEGKFARKFATKGASHTSQMDPLLGELTAELQGIKPTSPTCGIFSTVHEGRYIKPGGEPIHDVEYWKKGLRHSVYFTHGIRNAVDSGHTTFLELAPNPVALMQVALTTADAGLHDAQLIPTLARKQDEVSSMVSTMAQLYVYGHDLDIRTLFSRASGPQDYANIPPTRF 1062
                                   606       616       626       636       646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826       836       846       856       866       876       886       896       906       916       926       936       946       956       966       976       986       996      1006      1016      1026      1036      1046      1056

Chain C from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3tzy C    2 DKENFWGMAV   11
                                    11

Chain D from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .ee.....ee Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3tzy D    2 DKENFWGMAV   11
                                    11

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 '\|'

(no "SCOP Domain" information available for 3TZY)

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

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (O53579_MYCTO | O53579)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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:0019367	fatty acid elongation, saturated fatty acid	Elongation of a saturated fatty acid chain.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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.
	GO:0071769	mycolate cell wall layer assembly	The aggregation, arrangement and bonding together of a set of components, including arabinogalactan mycolate and trehalose dimycolate, to form the mycolate layer of the Actinobacterium-type cell wall. The mycolate layer is physically attached to the peptidoglycan layer.
	GO:0071768	mycolic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of mycolic acids, beta-hydroxy fatty acids with a long alpha-alkyl side chain.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
cellular component
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0034081	polyketide synthase complex	A protein complex that carries out enzymatic reactions involved in the biosynthesis of polyketides, any of a diverse group of natural products synthesized via linear poly-beta-ketones.

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	3tzy
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	O53579_MYCTO \| O53579	:	3tzw 3tzx 3tzz

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Ligands, Modified Residues, Ions (3, 11)

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