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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A (L64P MUTATION) IN COMPLEX WITH ATP

Authors :   E. S. Pilka, G. T. Kochan, C. Bhatia, F. Von Delft, C. H. Arrowsmith, A. M J. Weigelt, C. Bountra, U. Oppermann, Structural Genomics Consort

Date :   31 Jan 08 (Deposition) - 26 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Middle-Chain Acyl-Coa Synthetase, Xenobiotic/Medium-Chain Fatty Acid- Coa Ligase, Structural Genomics Consortium, Sgc, Atp-Binding, Fatty Acid Metabolism, Lipid Metabolism, Magnesium, Metal-Binding, Mitochondrion, Nucleotide-Binding Polymorphism, Transit Peptide, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Kochan, E. S. Pilka, F. Von Delft, U. Oppermann, W. W. Yue
Structural Snapshots For The Conformation-Dependent Catalysis By Human Medium-Chain Acyl-Coenzyme A Synthetase Acsm2A.
J. Mol. Biol. V. 388 997 2009
PubMed-ID: 19345228 | Reference-DOI: 10.1016/J.JMB.2009.03.064

Molecule 1 - ACYL-COENZYME A SYNTHETASE ACSM2A, MITOCHONDRIAL PRECURSOR
	Chains	:	A
	EC Number	:	6.2.1.2
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Strain	:	HIGH FIVE
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 32-577
	Gene	:	ACSM2A, ACSM2, MACS2
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A, MIDDLE- CHAIN ACYL-COA SYNTHETASE 2A, BUTYRATE-COA LIGASE 2A, BUTYRYL COENZYME A SYNTHETASE 2A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	2	Ligand/Ion	MAGNESIUM ION
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6	UNL	4	Ligand/Ion	UNKNOWN LIGAND

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	MET A:483 , HIS A:485 , VAL A:488 , HOH A:1179 , HOH A:1365	BINDING SITE FOR RESIDUE MG A 701
2	AC2	SOFTWARE	ATP A:801 , HOH A:911 , HOH A:912 , HOH A:913 , HOH A:915 , HOH A:916	BINDING SITE FOR RESIDUE MG A 702
3	AC3	SOFTWARE	LEU A:288 , PRO A:289 , LYS A:290 , PHE A:291 , HOH A:1002	BINDING SITE FOR RESIDUE CL A 703
4	AC4	SOFTWARE	ARG A:316 , LEU A:342 , THR A:345	BINDING SITE FOR RESIDUE CL A 704
5	AC5	SOFTWARE	THR A:221 , SER A:222 , GLY A:223 , THR A:224 , SER A:225 , LYS A:229 , GLY A:338 , GLU A:339 , SER A:340 , GLU A:359 , SER A:360 , TYR A:361 , GLY A:362 , GLN A:363 , THR A:364 , ASP A:446 , PHE A:458 , ARG A:461 , LYS A:557 , MG A:702 , HOH A:910 , HOH A:911 , HOH A:912 , HOH A:913 , HOH A:914 , HOH A:915 , HOH A:916 , HOH A:946 , HOH A:1067 , HOH A:1413 , HOH A:1457 , HOH A:1461	BINDING SITE FOR RESIDUE ATP A 801
6	AC6	SOFTWARE	LEU A:79 , MET A:80 , TRP A:81 , GLU A:85 , ASN A:89 , HOH A:998	BINDING SITE FOR RESIDUE TRS A 802
7	AC7	SOFTWARE	TRP A:71 , VAL A:116 , PRO A:117 , GLU A:118 , LYS A:195 , HOH A:1104 , HOH A:1108	BINDING SITE FOR RESIDUE GOL A 803

(no "SS Bond" information available for 3C5E)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:415	-	Pro A:416

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_058692	V	335	L	ACS2A_HUMAN	Polymorphism	4643305	A	V	335	L
2	UniProt	VAR_058693	T	336	A	ACS2A_HUMAN	Polymorphism	5002299	A	T	336	A
3	UniProt	VAR_058694	V	337	G	ACS2A_HUMAN	Polymorphism	4586421	A	V	337	G
4	UniProt	VAR_035247	S	513	L	ACS2A_HUMAN	Polymorphism	1133607	A	S	513	L
5	UniProt	VAR_035248	A	561	T	ACS2A_HUMAN	Polymorphism	1054977	A	A	561	T

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMP_BINDING	PS00455	Putative AMP-binding domain signature.	ACS2A_HUMAN	218-229	1	A:218-229

Asymmetric/Biological Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000396104	2a	ENSE00001773140	chr16:20471426-20471613	188	ACS2A_HUMAN	1-59	59	1	A:34-59	26
1.3	ENST00000396104	3	ENSE00001682005	chr16:20476839-20477049	211	ACS2A_HUMAN	60-130	71	1	A:60-130	71
1.4	ENST00000396104	4	ENSE00001771411	chr16:20480834-20481041	208	ACS2A_HUMAN	130-199	70	1	A:130-199	70
1.6b	ENST00000396104	6b	ENSE00001731165	chr16:20482395-20482538	144	ACS2A_HUMAN	199-247	49	1	A:199-247	49
1.7	ENST00000396104	7	ENSE00001594810	chr16:20482858-20483011	154	ACS2A_HUMAN	247-298	52	1	A:247-298	52
1.8	ENST00000396104	8	ENSE00001697128	chr16:20486684-20486763	80	ACS2A_HUMAN	299-325	27	1	A:299-325	27
1.9	ENST00000396104	9	ENSE00001626853	chr16:20486972-20487095	124	ACS2A_HUMAN	325-366	42	1	A:325-366	42
1.10	ENST00000396104	10	ENSE00001780247	chr16:20488691-20488771	81	ACS2A_HUMAN	367-393	27	1	A:367-393	27
1.11	ENST00000396104	11	ENSE00000516753	chr16:20489898-20489999	102	ACS2A_HUMAN	394-427	34	1	A:394-427	34
1.12	ENST00000396104	12	ENSE00001611767	chr16:20491895-20492022	128	ACS2A_HUMAN	428-470	43	1	A:428-470	43
1.13	ENST00000396104	13	ENSE00001600227	chr16:20492144-20492243	100	ACS2A_HUMAN	470-503	34	1	A:470-503	34
1.14	ENST00000396104	14	ENSE00001682277	chr16:20494380-20494499	120	ACS2A_HUMAN	504-543	40	1	A:504-543	40
1.15b	ENST00000396104	15b	ENSE00001523880	chr16:20497896-20498989	1094	ACS2A_HUMAN	544-577	34	1	A:544-569	26

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:536
 aligned with ACS2A_HUMAN | Q08AH3 from UniProtKB/Swiss-Prot  Length:577

    Alignment length:536
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563      
          ACS2A_HUMAN    34 QWGHQEVPAKFNFASDVLDHWADMEKAGKRLPSPALWWVNGKGKELMWNFRELSENSQQAANVLSGACGLQRGDRVAVVLPRVPEWWLVILGCIRAGLIFMPGTIQMKSTDILYRLQMSKAKAIVAGDEVIQEVDTVASECPSLRIKLLVSEKSCDGWLNFKKLLNEASTTHHCVETGSQEASAIYFTSGTSGLPKMAEHSYSSLGLKAKMDAGWTGLQASDIMWTISDTGWILNILCSLMEPWALGACTFVHLLPKFDPLVILKTLSSYPIKSMMGAPIVYRMLLQQDLSSYKFPHLQNCVTVGESLLPETLENWRAQTGLDIRESYGQTETGLTCMVSKTMKIKPGYMGTAASCYDVQIIDDKGNVLPPGTEGDIGIRVKPIRPIGIFSGYVDNPDKTAANIRGDFWLLGDRGIKDEDGYFQFMGRANDIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK 569
               SCOP domains d3c5ea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3c5eA02 A:466-569  [code=3.30.300.30, no name defined]                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh......eeeeee.....eeeeehhhhhhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhh....eeeee........eehhhhhhhh.............eeeeee.........eeeeehhhhhhhhhhhh.........eeee.....hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhh...eeeehhhhhhhhhh............eeeee....hhhhhhhhhhhhh...eeeeee...eeeee.............ee.....eeee............eeeeee...........ee..hhhhhhhhee..eeeeeeeeee.....eeeeee.hhheee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee.hhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------LAG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L-----------------------------------------------T-------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AMP_BINDING ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:34-59   Exon 1.3  PDB: A:60-130 UniProt: 60-130                                --------------------------------------------------------------------Exon 1.6b  PDB: A:199-247 UniProt: 199-247       ---------------------------------------------------Exon 1.8  PDB: A:299-325   -----------------------------------------Exon 1.10  PDB: A:367-393  Exon 1.11  PDB: A:394-427         Exon 1.12  PDB: A:428-470 UniProt: 428-470 ---------------------------------Exon 1.14  PDB: A:504-543               Exon 1.15b  PDB: A:544-569 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:130-199 UniProt: 130-199                             -----------------------------------------------Exon 1.7  PDB: A:247-298 UniProt: 247-298           --------------------------Exon 1.9  PDB: A:325-366 UniProt: 325-366 -------------------------------------------------------------------------------------------------------Exon 1.13  PDB: A:470-503         ------------------------------------------------------------------ Transcript 1 (2)
                 3c5e A  34 QWGHQEVPAKFNFASDVLDHWADMEKAGKRPPSPALWWVNGKGKELMWNFRELSENSQQAANVLSGACGLQRGDRVAVVLPRVPEWWLVILGCIRAGLIFMPGTIQMKSTDILYRLQMSKAKAIVAGDEVIQEVDTVASECPSLRIKLLVSEKSCDGWLNFKKLLNEASTTHHCVETGSQEASAIYFTSGTSGLPKMAEHSYSSLGLKAKMDAGWTGLQASDIMWTISDTGWILNILCSLMEPWALGACTFVHLLPKFDPLVILKTLSSYPIKSMMGAPIVYRMLLQQDLSSYKFPHLQNCVTVGESLLPETLENWRAQTGLDIRESYGQTETGLTCMVSKTMKIKPGYMGTAASCYDVQIIDDKGNVLPPGTEGDIGIRVKPIRPIGIFSGYVDNPDKTAANIRGDFWLLGDRGIKDEDGYFQFMGRADDIINSSGYRIGPSEVENALMEHPAVVETAVISSPDPVRGEVVKAFVVLASQFLSHDPEQLTKELQQHVKSVTAPYKYPRKIEFVLNLPKTVTGKIQRAKLRDKEWK 569
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Acetyl-CoA synthetase-like (64)

Superfamily: Acetyl-CoA synthetase-like (64)

Family: automated matches (26)

Protein domain: automated matches (26)

Human (Homo sapiens) [TaxId: 9606] (7)

d3c5ea_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: GMP Synthetase; Chain A, domain 3 (192)

Homologous Superfamily: [code=3.30.300.30, no name defined] (30)

Human (Homo sapiens) (5)

3c5eA02

A:466-569

(no "Pfam Domain" information available for 3C5E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ACS2A_HUMAN | Q08AH3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0047760	butyrate-CoA ligase activity	Catalysis of the reaction: ATP + an acid + CoA = AMP + diphosphate + an acyl-CoA.
	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:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	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:0042593	glucose homeostasis	Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
	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:0036112	medium-chain fatty-acyl-CoA metabolic process	The chemical reactions and pathways involving medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12.
	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:0070328	triglyceride homeostasis	Any process involved in the maintenance of an internal steady state of triglyceride within an organism or cell.
cellular component
	GO:0005759	mitochondrial matrix	The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Lys A:415 - Pro A:416	[ RasMol ]

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	ACS2A_HUMAN \| Q08AH3	:	2vze 2wd9 3b7w 3day 3eq6 3gpc

3b7w	CRYSTAL STRUCTURE OF L64P MUTANT OF HUMAN ACYL-COA SYNTHETASE MEDIUM-CHAIN FAMILY MEMBER 2A, APO STRUCTURE

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (6, 11)

Sites (7, 7)

SS Bonds (0, 0)

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