3K2I - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   HUMAN ACYL-COENZYME A THIOESTERASE 4

Authors :   M. I. Siponen, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, A. Kallas, T. Karlberg, P. Kraulis, T. Kotenyova, A. Kotzsch, N. Markova, T. K. Nielsen, P. Nordlund, T. Nyman, C. Persson, A. K. Roos, P. Schutz, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, E. Wahlberg, J. Weigelt, M. Welin, M. Wisniewska, H. Schuler, Structural Genomics Consortium (Sgc)

Date :   30 Sep 09 (Deposition) - 20 Oct 09 (Release) - 20 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Alpha/Beta Hydrolase Fold Seven-Stranded Beta-Sandwich, Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase, Peroxisome, Polymorphism, Serine Esterase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. I. Siponen, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, A. Kallas, T. Karlberg, P. Kraulis, T. Kotenyova, A. Kotzsch, N. Markova, T. K. Nielsen, P. Nordlund, T. Nyman, C. Persson, A. K. Roos, P. Schutz, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, E. Wahlberg, J. Weigelt, M. Welin, M. Wisniewska, H. Schuler
Human Acyl-Coenzyme A Thioesterase 4
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ACYL-COENZYME A THIOESTERASE 4
	Chains	:	A, B
	EC Number	:	3.1.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3) GOLD PRARE2
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ACOT4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACYL-COA THIOESTERASE 4, PEROXISOMAL ACYL COENZYME A THIOESTER HYDROLASE IB, PEROXISOMAL LONG-CHAIN ACYL-COA THIOESTERASE IB, PTE-IB, PTE-2B

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	NI	2	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU B:289	BINDING SITE FOR RESIDUE NI A 422
2	AC2	SOFTWARE	HOH A:492	BINDING SITE FOR RESIDUE CL A 423
3	AC3	SOFTWARE	HOH B:526	BINDING SITE FOR RESIDUE CL B 423

(no "SS Bond" information available for 3K2I)

Asymmetric Unit

No.	Residues
1	Glu A:8	-	Pro A:9
2	Gly A:155	-	Pro A:156
3	Gly A:223	-	Pro A:224
4	Glu B:8	-	Pro B:9
5	Gly B:155	-	Pro B:156
6	Gly B:223	-	Pro B:224

Asymmetric Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052300	R	57	C	ACOT4_HUMAN	Polymorphism	3742819	A/B	C	57	C
2	UniProt	VAR_052301	A	187	D	ACOT4_HUMAN	Polymorphism	35724886	A/B	A	187	D

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

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052300	R	57	C	ACOT4_HUMAN	Polymorphism	3742819	A	C	57	C
2	UniProt	VAR_052301	A	187	D	ACOT4_HUMAN	Polymorphism	35724886	A	A	187	D

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

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052300	R	57	C	ACOT4_HUMAN	Polymorphism	3742819	B	C	57	C
2	UniProt	VAR_052301	A	187	D	ACOT4_HUMAN	Polymorphism	35724886	B	A	187	D

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

Biological Unit 3 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_052300	R	57	C	ACOT4_HUMAN	Polymorphism	3742819	A/B	C	57	C
2	UniProt	VAR_052301	A	187	D	ACOT4_HUMAN	Polymorphism	35724886	A/B	A	187	D

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

(no "PROSITE Motif" information available for 3K2I)

(no "Exon" information available for 3K2I)

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:405
 aligned with ACOT4_HUMAN | Q8N9L9 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:408
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402        
          ACOT4_HUMAN     3 ATLILEPPGRCCWNEPVRIAVRGLAPEQRVTLRASLRDEKGALFRAHARYCADARGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVVELEVLDGHDPEPGRLLCQAQHERHFLPPGVRRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYRASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASFLKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKAQGPILLIVGQDDHNWRSELYAQTVSERLQAHGKEKPQIICYPGTGHYIEPPYFPLCPASLHRLLNKHVIWGGEPRAHSKAQEDAWKQILAFFCKHL 410
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.---.......eeeee......eeeeeeeee.....eeeeeeeee......ee.......ee.......hhhhhh.ee...............eeeeeeeee........eeeeeeeee.......eeeeeee..eeeeeee........eeeee........hhhhhhhhh...eeeeee.............eehhhhhhhhhhhhh........eeeeeehhhhhhhhhhhhhh..eeeeeee..........eee..eee.....hhhhhee.....ee.........hhhhh....hhhhh...eeeeee......hhhhhhhhhhhhhhhh.....eeeee................eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k2i A   3 ATLILEP---CCWNEPVRIAVRGLAPEQRVTLRASLRDEKGALFRAHARYCADACGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVVELEVLDGHDPEPGRLLCQAQHERHFLPPGVWRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYRASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASFLKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKAQGPILLIVGQDDHNWRSELYAQTVSERLQAHGKEKPQIICYPGTGHYIEPPYFPLCPASLHRLLNKHVIWGGEPRAHSKAQEDAWKQILAFFCKHL 410
                                  |  -|       22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402        
                                  9  13

Chain B from PDB  Type:PROTEIN  Length:405
 aligned with ACOT4_HUMAN | Q8N9L9 from UniProtKB/Swiss-Prot  Length:421

    Alignment length:408
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402        
          ACOT4_HUMAN     3 ATLILEPPGRCCWNEPVRIAVRGLAPEQRVTLRASLRDEKGALFRAHARYCADARGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVVELEVLDGHDPEPGRLLCQAQHERHFLPPGVRRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYRASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASFLKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKAQGPILLIVGQDDHNWRSELYAQTVSERLQAHGKEKPQIICYPGTGHYIEPPYFPLCPASLHRLLNKHVIWGGEPRAHSKAQEDAWKQILAFFCKHL 410
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ------------Bile_Hydr_Trans-3k2iB03 B:15-142                                                                                                ------------------------------------------------------------BAAT_C-3k2iB01 B:203-410                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ------------Bile_Hydr_Trans-3k2iB04 B:15-142                                                                                                ------------------------------------------------------------BAAT_C-3k2iB02 B:203-410                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .eeeee.---.......eeeee......eeeeeeeee.....eeeeeeeee......ee.......ee.......hhhhhh.ee...............eeeeeeeee........eeeeeeeee.......eeeeeee..eeeeeee........eeeee........hhhhhhhhh...eeeee..............eehhhhhhhhhhhhhh.......eeeeeehhhhhhhhhhhhhh..eeeeeee..........eee..eee.....hhhhhee.....ee.........hhhhh....hhhhh...eeeeee......hhhhhhhhhhhhhhhh.....eeeee................eeee....eeee...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------C---------------------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3k2i B   3 ATLILEP---CCWNEPVRIAVRGLAPEQRVTLRASLRDEKGALFRAHARYCADACGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVVELEVLDGHDPEPGRLLCQAQHERHFLPPGVWRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYRASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASFLKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKAQGPILLIVGQDDHNWRSELYAQTVSERLQAHGKEKPQIICYPGTGHYIEPPYFPLCPASLHRLLNKHVIWGGEPRAHSKAQEDAWKQILAFFCKHL 410
                                  |  -|       22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402        
                                  9  13

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 3K2I)

(no "CATH Domain" information available for 3K2I)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: AB_hydrolase (347)

Family: BAAT_C (1)

Homo sapiens (Human) (1)

1a	BAAT_C-3k2iB01	B:203-410
1b	BAAT_C-3k2iB02	B:203-410

Clan: no clan defined [family: Bile_Hydr_Trans] (1)

Family: Bile_Hydr_Trans (1)

Homo sapiens (Human) (1)

2a	Bile_Hydr_Trans-3k2iB03	B:15-142
2b	Bile_Hydr_Trans-3k2iB04	B:15-142

Asymmetric Unit(hide GO term definitions)

Chain A,B (ACOT4_HUMAN | Q8N9L9)

molecular function
	GO:0047617	acyl-CoA hydrolase activity	Catalysis of the reaction: acyl-CoA + H2O = CoA + a carboxylate.
	GO:0052689	carboxylic ester hydrolase activity	Catalysis of the hydrolysis of a carboxylic ester bond.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016290	palmitoyl-CoA hydrolase activity	Catalysis of the reaction: palmitoyl-CoA + H2O = CoA + palmitate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	GO:0004778	succinyl-CoA hydrolase activity	Catalysis of the reaction: H(2)O + succinyl-CoA = CoA + H(+) + succinate.
	GO:0016790	thiolester hydrolase activity	Catalysis of the reaction: RCO-SR' + H2O = RCOOH + HSR'. This reaction is the hydrolysis of a thiolester bond, an ester formed from a carboxylic acid and a thiol (i.e., RCO-SR'), such as that found in acetyl-coenzyme A.
biological process
	GO:0006637	acyl-CoA metabolic process	The chemical reactions and pathways involving acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with an acyl group.
	GO:0019605	butyrate metabolic process	The chemical reactions and pathways involving any butyrate, the anions of butyric acid (butanoic acid), a saturated, unbranched aliphatic acid.
	GO:0043649	dicarboxylic acid catabolic process	The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups.
	GO:0043648	dicarboxylic acid metabolic process	The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-).
	GO:0001676	long-chain fatty acid metabolic process	The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
	GO:0035338	long-chain fatty-acyl-CoA biosynthetic process	The chemical reactions and pathways resulting in the formation of a long-chain fatty-acyl-CoA any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. Long-chain fatty-acyl-CoAs have chain lengths of C13 or more.
	GO:0032788	saturated monocarboxylic acid metabolic process	The chemical reactions and pathways involving saturated monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-) and fully saturated C-C bonds.
	GO:0046459	short-chain fatty acid metabolic process	The chemical reactions and pathways involving fatty acids with a chain length of less than C6.
	GO:0006104	succinyl-CoA metabolic process	The chemical reactions and pathways involving succinyl-CoA, a compound composed of the monovalent acyl group 3-carboxypropanoyl, derived from succinic acid by loss of one OH group, linked to coenzyme A.
	GO:0032789	unsaturated monocarboxylic acid metabolic process	The chemical reactions and pathways involving unsaturated monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-) and one or more unsaturated C-C bonds.
	GO:0000038	very long-chain fatty acid metabolic process	The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22.
cellular component
	GO:0005782	peroxisomal matrix	The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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	Cis Peptide Bonds
		Glu A:8 - Pro A:9	[ RasMol ]
		Glu B:8 - Pro B:9	[ RasMol ]
		Gly A:155 - Pro A:156	[ RasMol ]
		Gly A:223 - Pro A:224	[ RasMol ]
		Gly B:155 - Pro B:156	[ RasMol ]
		Gly B:223 - Pro B:224	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 5)

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SS Bonds (0, 0)

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