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Asym./Biol. Unit (Jmol Viewer)

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Title :   E. COLI BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE MODIFIED BY ITS CLASSIC MECHANISM-BASED INACTIVATOR, 3-DECYNOYL-N-ACETYL CYSTEAMINE

Authors :   M. Leesong

Date :   08 Jan 96 (Deposition) - 11 Jul 96 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Fatty Acid Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Leesong, B. S. Henderson, J. R. Gillig, J. M. Schwab, J. L. Smith
Structure Of A Dehydratase-Isomerase From The Bacterial Pathway For Biosynthesis Of Unsaturated Fatty Acids: Two Catalytic Activities In One Active Site.
Structure V. 4 253 1996
PubMed-ID: 8805534 | Reference-DOI: 10.1016/S0969-2126(96)00030-5
(for further references see the PDB file header)

Molecule 1 - BETA-HYDROXYDECANOYL THIOL ESTER DEHYDRASE
	Chains	:	A, B
	EC Number	:	4.2.1.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Gene	:	FABA
	Expression System Plasmid	:	PRA244
	Expression System Taxid	:	562
	Expression System Vector Type	:	BACTERIAL
	Gene	:	FABA
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	TAC PROMOTER
	Strain	:	RA244
	Synonym	:	BETA-HYDROXYDECANOYL ACP DEHYDRASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	DAC	2	Ligand/Ion	2-DECENOYL N-ACETYL CYSTEAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	UNKNOWN	HIS A:70 , ASP B:84	TWO POLAR RESIDUES ARE FOUND IN THE CATALYTIC REGION OF THE ACTIVE SITE.
2	AC2	UNKNOWN	HIS B:70 , ASP A:84	TWO POLAR RESIDUES ARE FOUND IN THE CATALYTIC REGION OF THE ACTIVE SITE.
3	AC3	SOFTWARE	HIS A:70 , PHE A:71 , MET A:77 , GLY A:79 , PHE A:113 , GLY A:115 , GLN B:27 , TRP B:87 , GLY B:91 , ARG B:104 , ALA B:105 , LEU B:106 , PHE B:171	BINDING SITE FOR RESIDUE DAC A 172
4	AC4	SOFTWARE	GLN A:27 , GLY A:91 , ARG A:104 , ALA A:105 , LEU A:106 , PHE A:171 , HIS B:70 , PHE B:71 , MET B:77 , GLY B:79 , PHE B:113 , GLY B:115 , GLN B:116	BINDING SITE FOR RESIDUE DAC B 172

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:31	-	Asn A:32
2	His A:70	-	Phe A:71
3	Pro B:31	-	Asn B:32
4	His B:70	-	Phe B:71

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_FABA_ECOLI_001 *	P	76	L	FABA_ECOLI	---	---	A/B	P	75	L
2	UniProt	VAR_FABA_ECOLI_002 *	G	102	D	FABA_ECOLI	---	---	A/B	G	101	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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

(no "Exon" information available for 1MKA)

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:171
 aligned with FABA_ECOLI | P0A6Q3 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
           FABA_ECOLI     2 VDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDTSAF 172
               SCOP domains d1mkaa_ A: beta-Hydroxydecanol thiol ester dehydrase                                                                                                                        SCOP domains
               CATH domains 1mkaA00 A:1-171  [code=3.10.129.10, no name defined]                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ....----hhhhhhhhh...................eeeeeee........eeeeeeeee....hhhhh.........hhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee.......eeeeeeeeeeeeeee.eeeeeeeeeeeee.eeeeeeeeeeeeee...... Sec.struct. author (1)
     Sec.struct. author (2) ----eeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------L-------------------------D---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mka A   1 VDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDTSAF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

Chain B from PDB  Type:PROTEIN  Length:171
 aligned with FABA_ECOLI | P0A6Q3 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
           FABA_ECOLI     2 VDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDTSAF 172
               SCOP domains d1mkab_ B: beta-Hydroxydecanol thiol ester dehydrase                                                                                                                        SCOP domains
               CATH domains 1mkaB00 B:1-171  [code=3.10.129.10, no name defined]                                                                                                                        CATH domains
           Pfam domains (1) ---------------------------FabA-1mkaB01 B:28-158                                                                                                              ------------- Pfam domains (1)
           Pfam domains (2) ---------------------------FabA-1mkaB02 B:28-158                                                                                                              ------------- Pfam domains (2)
     Sec.struct. author (1) ....----hhhhhhhhh...................eeeeeee........eeeeeeeee....hhhhh.........hhhhhhhhhhhhhhhhhh.....eeeeeeeeeeeee.......eeeeeeeeeeeeeee.eeeeeeeeeeeee.eeeeeeeeeeeeee...... Sec.struct. author (1)
     Sec.struct. author (2) ----eeeee------------------------------------------------------------------------------------------------------------------------------------------------------------------ Sec.struct. author (2)
                 SAPs(SNPs) --------------------------------------------------------------------------L-------------------------D---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mka B   1 VDKRESYTKEDLLASGRGELFGAKGPQLPAPNMLMMDRVVKMTETGGNFDKGYVEAELDINPDLWFFGCHFIGDPVMPGCLGLDAMWQLVGFYLGWLGGEGKGRALGVGEVKFTGQVLPTAKKVTYRIHFKRIVNRRLIMGLADGEVLVDGRLIYTASDLKVGLFQDTSAF 171
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170

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) (23004)

Fold: Thioesterase/thiol ester dehydrase-isomerase (151)

Superfamily: Thioesterase/thiol ester dehydrase-isomerase (151)

Family: beta-Hydroxydecanol thiol ester dehydrase (11)

Protein domain: beta-Hydroxydecanol thiol ester dehydrase (4)

Escherichia coli [TaxId: 562] (4)

1a	d1mkaa_	A:
1b	d1mkab_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Thiol Ester Dehydrase; Chain A (90)

Homologous Superfamily: [code=3.10.129.10, no name defined] (90)

Escherichia coli. Organism_taxid: 562. Strain: ra244. (2)

1a	1mkaA00	A:1-171
1b	1mkaB00	B:1-171

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HotDog (52)

Family: FabA (8)

Escherichia coli (strain K12) (2)

1a	FabA-1mkaB01	B:28-158
1b	FabA-1mkaB02	B:28-158

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (FABA_ECOLI | P0A6Q3)

molecular function
	GO:0019171	3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity	Catalysis of the reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = H2O + a trans-delta2-enoyl-acyl-[acyl-carrier protein].
	GO:0008693	3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity	Catalysis of the reaction: (3R)-3-hydroxydecanoyl-[acyl-carrier protein] = 2,3-decenoyl-[acyl-carrier protein] or 3,4-decenoyl-[acyl-carrier protein] + H2O.
	GO:0047451	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity	Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + 2-octenoyl-[acyl-carrier protein].
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0034017	trans-2-decenoyl-acyl-carrier-protein isomerase activity	Catalysis of the reaction: trans-dec-2-enoyl-[acyl-carrier protein] = cis-dec-3-enoyl-[acyl-carrier protein].
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:0008610	lipid biosynthetic process	The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	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.
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/Biological Unit
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	Cis Peptide Bonds
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		Pro A:31 - Asn A:32	[ RasMol ]
		Pro B:31 - Asn B:32	[ RasMol ]

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	1mka
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

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