4B0I - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) MUTANT (H70N) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-HYDROXYDECANOYL-N-ACETYL CYSTEAMINE

Authors :   L. Moynie, S. A. Mcmahon, S. M. Leckie, F. G. Duthie, A. Koehnke, J. H. Nai

Date :   02 Jul 12 (Deposition) - 28 Nov 12 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.03

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: C,D  (1x)
Biol. Unit 2: A,B  (1x)
Biol. Unit 3: E  (2x)

Keywords :   Lyase, Fatty Acid Biosynthesis, Bacterial Virulence, Drug Discovery (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Moynie, S. M. Leckie, S. A. Mcmahon, F. G. Duthie, A. Koehnke, J. W. Taylor, M. S. Alphey, R. Brenk, A. D. Smith, J. H. Naismith
Structural Insights Into The Mechanism And Inhibition Of The Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase From Pseudomonas Aeruginosa
J. Mol. Biol. V. 425 365 2013
PubMed-ID: 23174186 | Reference-DOI: 10.1016/J.JMB.2012.11.017

Molecule 1 - 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE
	Chains	:	A, B, C, D, E
	EC Number	:	4.2.1.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST14
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	STAR
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PA01
	Synonym	:	BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:			C	D
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (2x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	KBP	5	Ligand/Ion	S-[2-(ACETYLAMINO)ETHYL] (3R)-3-HYDROXYDECANETHIOATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	KBP	2	Ligand/Ion	S-[2-(ACETYLAMINO)ETHYL] (3R)-3-HYDROXYDECANETHIOATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	KBP	2	Ligand/Ion	S-[2-(ACETYLAMINO)ETHYL] (3R)-3-HYDROXYDECANETHIOATE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	KBP	2	Ligand/Ion	S-[2-(ACETYLAMINO)ETHYL] (3R)-3-HYDROXYDECANETHIOATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:27 , LEU A:28 , ASP A:84 , TRP A:87 , GLN A:88 , GLY A:91 , PHE A:92 , ARG A:104 , ALA A:105 , HOH A:2046 , HOH A:2047 , HOH A:2085 , MET B:77 , PRO B:78 , GLY B:79 , GLY B:115 , GLN B:116	BINDING SITE FOR RESIDUE KBP A1170
2	AC2	SOFTWARE	PHE A:71 , MET A:77 , PRO A:78 , GLY A:79 , GLY A:115 , GLN A:116 , HOH A:2043 , HOH A:2045 , GLN B:27 , ASP B:84 , GLN B:88 , GLY B:91 , PHE B:92 , ARG B:104 , ALA B:105 , PHE B:171	BINDING SITE FOR RESIDUE KBP B1172
3	AC3	SOFTWARE	GLN C:27 , LEU C:28 , ASP C:84 , TRP C:87 , GLN C:88 , GLY C:91 , PHE C:92 , ARG C:104 , ALA C:105 , PHE C:171 , HOH C:2061 , HOH C:2091 , ASN D:70 , MET D:77 , PRO D:78 , GLY D:79 , GLY D:115 , GLN D:116	BINDING SITE FOR RESIDUE KBP C1172
4	AC4	SOFTWARE	ASN C:70 , PHE C:71 , PRO C:78 , GLY C:79 , GLY C:115 , GLN C:116 , HOH C:2052 , HOH C:2058 , HOH C:2060 , GLN D:27 , LEU D:28 , ASP D:84 , TRP D:87 , GLN D:88 , GLY D:91 , PHE D:92 , ARG D:104 , ALA D:105 , PHE D:171	BINDING SITE FOR RESIDUE KBP D1172
5	AC5	SOFTWARE	ALA E:26 , GLN E:27 , LEU E:28 , ASN E:70 , PHE E:71 , MET E:77 , PRO E:78 , GLY E:79 , ASP E:84 , GLN E:88 , GLY E:91 , PHE E:92 , ARG E:104 , ALA E:105 , GLY E:115 , GLN E:116 , PHE E:171 , HOH E:2024 , HOH E:2027 , HOH E:2028	BINDING SITE FOR RESIDUE KBP E1172

(no "SS Bond" information available for 4B0I)

Asymmetric Unit

No.	Residues
1	Pro A:31	-	Asn A:32
2	Asn A:70	-	Phe A:71
3	Pro B:31	-	Asn B:32
4	Asn B:70	-	Phe B:71
5	Pro C:31	-	Asn C:32
6	Asn C:70	-	Phe C:71
7	Pro D:31	-	Asn D:32
8	Asn D:70	-	Phe D:71
9	Pro E:31	-	Asn E:32
10	Asn E:70	-	Phe E:71

(no "SAP(SNP)/Variant" information available for 4B0I)

(no "PROSITE Motif" information available for 4B0I)

(no "Exon" information available for 4B0I)

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:168
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:168
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161        
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTD 169
               SCOP domains d4b0ia_ A: automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..............eeeeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4b0i A   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACNFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTD 169
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:170
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0ib_ B: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..............................................hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............eee......................................eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0i B   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACNFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain C from PDB  Type:PROTEIN  Length:170
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0ic_ C: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhh....eeeeeee..............eeeeeeeeeeee....eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0i C   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACNFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain D from PDB  Type:PROTEIN  Length:170
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:170
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171
           FABA_PSEAE     2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0id_ D: automated matches                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhh..............................................hhhhhhh.......hhhhhhhhhhhhhhhhhhhh.............eee......................................eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0i D   2 TKQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACNFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171

Chain E from PDB  Type:PROTEIN  Length:167
 aligned with FABA_PSEAE | O33877 from UniProtKB/Swiss-Prot  Length:171

    Alignment length:169
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162         
           FABA_PSEAE     3 KQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACHFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTINRSLVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
               SCOP domains d4b0ie_ E: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh....................eeeeee.........eeeeeee....hhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...eeeeee...eee.........eeeeeeeeeeee.--.eeeeeeeeeee..eeeeeeeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4b0i E   3 KQHAFTREDLLRCSRGELFGPGNAQLPAPNMLMIDRIVHISDVGGKYGKGELVAELDINPDLWFFACNFEGDPVMPGCLGLDAMWQLVGFYLGWQGNPGRGRALGSGEVKFFGQVLPTAKKVTYNIHIKRTIN--LVLAIADGTVSVDGREIYSAEGLRVGLFTSTDSF 171
                                    12        22        32        42        52        62        72        82        92       102       112       122       132  |  | 142       152       162         
                                                                                                                                                              135  |                                 
                                                                                                                                                                 138

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(

)

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: automated matches (7)

Pseudomonas aeruginosa [TaxId: 208964] (6)

1a	d4b0ia_	A:
1b	d4b0ib_	B:
1c	d4b0ic_	C:
1d	d4b0id_	D:
1e	d4b0ie_	E:

(no "CATH Domain" information available for 4B0I)

(no "Pfam Domain" information available for 4B0I)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (FABA_PSEAE | O33877)

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: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:0006636	unsaturated fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of an unsaturated fatty acid, any fatty acid containing one or more double bonds between carbon atoms.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
		Asn A:70 - Phe A:71	[ RasMol ]
		Asn B:70 - Phe B:71	[ RasMol ]
		Asn C:70 - Phe C:71	[ RasMol ]
		Asn D:70 - Phe D:71	[ RasMol ]
		Asn E:70 - Phe E:71	[ RasMol ]
		Pro A:31 - Asn A:32	[ RasMol ]
		Pro B:31 - Asn B:32	[ RasMol ]
		Pro C:31 - Asn C:32	[ RasMol ]
		Pro D:31 - Asn D:32	[ RasMol ]
		Pro E:31 - Asn E:32	[ RasMol ]

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	FABA_PSEAE \| O33877	:	4b0b 4b0c 4b0j 4b8u 4cl6 4fq9

4b0b	CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-(PYRIDIN-2-YLOXY)ANILINE
4b0c	CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 3-(PENTYLTHIO)-4H-1,2,4-TRIAZOLE
4b0j	CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH 5-(2-THIENYL)-3-ISOXAZOLYL METHANOL
4b8u	CRYSTAL STRUCTURE OF 3-HYDROXYDECANOYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABA) FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH N-ISOBUTYL-2-(5-(2-THIENYL)-1,2- OXAZOL-3-YL-)METHOXY)ACETAMIDE
4fq9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 5)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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