1MZS - JenaLib

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Title :   CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III WITH BOUND DICHLOROBENZYLOXY-INDOLE-CARBOXYLIC ACID INHIBITOR

Authors :   R. A. Daines, I. Pendrak, K. Sham, G. S. Van Aller, A. K. Konstantinidis J. T. Lonsdale, C. A. Janson, X. Qui, M. Brandt, C. Silverman, M. S. Head

Date :   09 Oct 02 (Deposition) - 13 Nov 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Fabh, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. A. Daines, I. Pendrak, K. Sham, G. S. Van Aller, A. K. Konstantinidis, J. T. Lonsdale, C. A. Janson, X. Qiu, M. Brandt, S. S. Khandekar, C. Silverman, M. S. Head
First X-Ray Cocrystal Structure Of A Bacterial Fabh Condensing Enzyme And A Small Molecule Inhibitor Achieved Using Rational Design And Homology Modeling
J. Med. Chem. V. 46 5 2003
PubMed-ID: 12502353 | Reference-DOI: 10.1021/JM025571B

Molecule 1 - 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III
	Chains	:	A
	EC Number	:	2.3.1.41
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	BETA-KETOACYL-ACP SYNTHASE III, KAS III

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	669	1	Ligand/Ion	1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	669	1	Ligand/Ion	1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2	OCS	1	Mod. Amino Acid	CYSTEINESULFONIC ACID
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	669	2	Ligand/Ion	1-(5-CARBOXYPENTYL)-5-(2,6-DICHLOROBENZYLOXY)-1H-INDOLE-2-CARBOXYLIC ACID
2	OCS	2	Mod. Amino Acid	CYSTEINESULFONIC ACID
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:16 , ASP A:21 , GLU A:171	BINDING SITE FOR RESIDUE PO4 A 340
2	AC2	SOFTWARE	TRP A:32 , ARG A:36 , THR A:37 , PRO A:47 , OCS A:112 , ARG A:151 , GLY A:152 , LEU A:189 , MET A:207 , GLY A:209 , PHE A:213 , ALA A:216 , ALA A:246 , ASN A:247 , ILE A:250 , PHE A:304 , HOH A:519 , HOH A:528 , HOH A:546	BINDING SITE FOR RESIDUE 669 A 350

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

Asymmetric Unit

No.	Residues
1	Phe A:87	-	Pro A:88
2	Pro A:172	-	Gly A:173
3	Gly A:307	-	Phe A:308

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

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

(no "Exon" information available for 1MZS)

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:317
 aligned with FABH_ECOLI | P0A6R0 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:317
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
           FABH_ECOLI     1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAACAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
               SCOP domains d1mzsa1 A:1-174 Ketoacyl-ACP synthase III (FabH)                                                                                                                              d1mzsa2 A:175-317 Ketoacyl-ACP synthase III (FabH)                                                                                              SCOP domains
               CATH domains 1mzsA01 A:1-170  [code=3.40.47.10, no name defined]                                                                                                                       1mzsA02 A:171-317  [code=3.40.47.10, no name defined]                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------ACP_syn_III-1mzsA01 A:106-183                                                 --------------------------------------------ACP_syn_III_C-1mzsA02 A:228-317                                                            Pfam domains
         Sec.struct. author .eeeeeeeeee....eeehhhhhh....hhhhhhhhhh..eee......hhhhhhhhhhhhhhhhhh.hhhhh.eeeee.........hhhhhhhhhhh.....eeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeehhhhhh...hhhhhh....eeeeeeeeee....eeeeeeee.hhhhh.ee...............eehhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeee...hhhhhhhhhhhh..hhhhh..hhhhhh.hhhhhhhhhhhhhhhh.......eeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mzs A   1 MYTKIIGTGSYLPEQVRTNADLEKMVDTSDEWIVTRTGIRERHIAAPNETVSTMGFEAATRAIEMAGIEKDQIGLIVVATTSATHAFPSAACQIQSMLGIKGCPAFDVAAAcAGFTYALSVADQYVKSGAVKYALVVGSDVLARTCDPTDRGTIIIFGDGAGAAVLAASEEPGIISTHLHADGSYGELLTLPNADRVNPENSIHLTMAGNEVFKVAVTELAHIVDETLAANNLDRSQLDWLVPHQANLRIISATAKKLGMSMDNVVVTLDRHGNTSAASVPCALDEAVRDGRIKPGQLVLLEAFGGGFTWGSALVRF 317
                                    10        20        30        40        50        60        70        80        90       100       110 |     120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       
                                                                                                                                         112-OCS

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: Thiolase-like (231)

Superfamily: Thiolase-like (231)

Family: Chalcone synthase-like (56)

Protein domain: Ketoacyl-ACP synthase III (FabH) (22)

Escherichia coli [TaxId: 562] (9)

1a	d1mzsa1	A:1-174
1b	d1mzsa2	A:175-317

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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)

Escherichia coli. Organism_taxid: 562. (23)

1a	1mzsA01	A:1-170
1b	1mzsA02	A:171-317

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

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Clan: Thiolase (72)

Family: ACP_syn_III (12)

Escherichia coli (strain K12) (1)

ACP_syn_III-1mzsA01

A:106-183

Family: ACP_syn_III_C (12)

Escherichia coli (strain K12) (1)

ACP_syn_III_C-1mzsA02

A:228-317

Asymmetric Unit(hide GO term definitions)

Chain A (FABH_ECOLI | P0A6R0)

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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		669	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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	Cis Peptide Bonds
		Gly A:307 - Phe A:308	[ RasMol ]
		Phe A:87 - Pro A:88	[ RasMol ]
		Pro A:172 - Gly A:173	[ RasMol ]

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	1mzs
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	2.3.1.41
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	FABH_ECOLI \| P0A6R0	:	1ebl 1hn9 1hnd 1hnh 1hnj 1hnk 2eft 2gyo 3il9 4z8d 5bnm 5bnr 5bns

1hn9	CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III
1hnd	CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III-COA COMPLEX
1hnh	CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III AND DEGRADED FORM OF ACETYL-COA
1hnj	CRYSTAL STRUCTURE OF BETA-KETOACYL-ACP SYNTHASE III AND MALONYL-COA

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

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