2A1U - JenaLib

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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE HUMAN ETF E165BETAA MUTANT

Authors :   H. S. Toogood, A. Van Thiel, N. S. Scrutton, D. Leys

Date :   21 Jun 05 (Deposition) - 05 Jul 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.11

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

Keywords :   Electron Transfer, Mobile Domain, Conformational Sampling, Electron Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. S. Toogood, A. Van Thiel, N. S. Scrutton, D. Leys
Stabilization Of Non-Productive Conformations Underpins Rapid Electron Transfer To Electron-Transferring Flavoprotein
J. Biol. Chem. V. 280 30361 2005
PubMed-ID: 15975918 | Reference-DOI: 10.1074/JBC.M505562200
(for further references see the PDB file header)

Molecule 1 - ELECTRON TRANSFER FLAVOPROTEIN ALPHA-SUBUNIT, MITOCHONDRIAL PRECURSOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PK18
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALPHA-ETF

Molecule 2 - ELECTRON TRANSFER FLAVOPROTEIN BETA-SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PK18
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	BETA-ETF

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:208 , GLY A:222 , ARG A:223 , GLY A:224 , SER A:248 , ARG A:249 , ALA A:250 , GLN A:262 , VAL A:263 , GLY A:264 , GLN A:265 , THR A:266 , GLY A:267 , GLY A:279 , ILE A:280 , SER A:281 , GLN A:285 , HIS A:286 , ASN A:300 , LYS A:301 , ASP A:302 , ALA A:317 , ASP A:318 , LEU A:319 , HOH A:619 , HOH A:634 , LEU B:185	BINDING SITE FOR RESIDUE FAD A 599
2	AC2	SOFTWARE	ALA B:9 , VAL B:10 , LYS B:11 , ASN B:39 , CYS B:42 , CYS B:66 , VAL B:104 , LEU B:122 , GLY B:123 , GLN B:125 , ALA B:126 , ASP B:129 , CYS B:131 , ASN B:132 , GLN B:133 , THR B:134 , HOH B:617	BINDING SITE FOR RESIDUE AMP B 600

(no "SS Bond" information available for 2A1U)

Asymmetric/Biological Unit

No.	Residues
1	Leu B:177	-	Pro B:178

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002366	G	116	R	ETFA_HUMAN	Disease (GA2A)	119458971	A	G	116	R
2	UniProt	VAR_025804	D	128	N	ETFB_HUMAN	Disease (GA2B)	104894678	B	D	128	N
3	UniProt	VAR_008548	T	154	M	ETFB_HUMAN	Polymorphism	1130426	B	T	154	M
4	UniProt	VAR_002367	V	157	G	ETFA_HUMAN	Disease (GA2A)	119458969	A	V	157	G
5	UniProt	VAR_002369	R	164	Q	ETFB_HUMAN	Disease (GA2B)	104894677	B	R	164	Q
6	UniProt	VAR_008547	T	171	I	ETFA_HUMAN	Polymorphism	1801591	A	T	171	I
7	UniProt	VAR_002368	T	266	M	ETFA_HUMAN	Disease (GA2A)	119458970	A	T	266	M

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ETF_BETA	PS01065	Electron transfer flavoprotein beta-subunit signature.	ETFB_HUMAN	162-182	1	B:162-182
2	ETF_ALPHA	PS00696	Electron transfer flavoprotein alpha-subunit signature.	ETFA_HUMAN	274-300	1	A:274-300

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000309244	1	ENSE00001384271	chr19:51869672-51869524	149	ETFB_HUMAN	1-19	19	1	B:4-19	16
1.2b	ENST00000309244	2b	ENSE00001225639	chr19:51857562-51857404	159	ETFB_HUMAN	20-72	53	1	B:20-72	53
1.3	ENST00000309244	3	ENSE00000722381	chr19:51856544-51856386	159	ETFB_HUMAN	73-125	53	1	B:73-125	53
1.4	ENST00000309244	4	ENSE00000722391	chr19:51853645-51853583	63	ETFB_HUMAN	126-146	21	1	B:126-146	21
1.5	ENST00000309244	5	ENSE00000722401	chr19:51850312-51850154	159	ETFB_HUMAN	147-199	53	1	B:147-199	53
1.6	ENST00000309244	6	ENSE00001471664	chr19:51848635-51848410	226	ETFB_HUMAN	200-255	56	1	B:200-255	56

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:315
 aligned with ETFA_HUMAN | P13804 from UniProtKB/Swiss-Prot  Length:333

    Alignment length:315
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328     
           ETFA_HUMAN    19 FQSTLVIAEHANDSLAPITLNTITAATRLGGEVSCLVAGTKCDKVAQDLCKVAGIAKVLVAQHDVYKGLLPEELTPLILATQKQFNYTHICAGASAFGKNLLPRVAAKLEVAPISDIIAIKSPDTFVRTIYAGNALCTVKCDEKVKVFSVRGTSFDAAATSGGSASSEKASSTSPVEISEWLDQKLTKSDRPELTGAKVVVSGGRGLKSGENFKLLYDLADQLHAAVGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKTIVAINKDPEAPIFQVADYGIVADLFKVVPEMTEILKKK 333
               SCOP domains d2a1ua1 A:19-207 automated matches                                                                                                                                                           d2a1ua2 A:208-333 automated matches                                                                                            SCOP domains
               CATH domains 2a1uA01 A:19-204 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                    2a1uA02 A:205-333 TPP-binding domain                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...eeeeeeee..hhhhhhhhh......eeeeee.hhhh..hhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh...eeee.eeee..eeeeee....eeeeeee....eeeee.hhhh..........eeee.........eeeeeeee............eeeee.hhhh....hhhhhhhhhhhh.eeeehhhhhhh...hhhhh...........eeeee....hhhhhh......eeeeee....hhhhhh..eeee.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------R----------------------------------------G-------------I----------------------------------------------------------------------------------------------M------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_ALPHA  PDB: A:274-300  --------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a1u A  19 FQSTLVIAEHANDSLAPITLNTITAATRLGGEVSCLVAGTKCDKVAQDLCKVAGIAKVLVAQHDVYKGLLPEELTPLILATQKQFNYTHICAGASAFGKNLLPRVAAKLEVAPISDIIAIKSPDTFVRTIYAGNALCTVKCDEKVKVFSVRGTSFDAAATSGGSASSEKASSTSPVEISEWLDQKLTKSDRPELTGAKVVVSGGRGLKSGENFKLLYDLADQLHAAVGASRAAVDAGFVPNDMQVGQTGKIVAPELYIAVGISGAIQHLAGMKDSKTIVAINKDPEAPIFQVADYGIVADLFKVVPEMTEILKKK 333
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328

Chain B from PDB  Type:PROTEIN  Length:252
 aligned with ETFB_HUMAN | P38117 from UniProtKB/Swiss-Prot  Length:255

    Alignment length:252
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253  
           ETFB_HUMAN     4 LRVLVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSCGPAQCQETIRTALAMGADRGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVTLEGDKLKVEREIDGGLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKPGDLGVDLTSKLSVISVEDPPQRTAGVKVETTEDLVAKLKEIGRI 255
               SCOP domains d2a1ub_ B: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2a1uB00 B:4-255 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eee.....................eeehhhhhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhh..eeeeee.hhhhhh..hhhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhh..eeeeeeeeee...eeeeeeee..eeeeeeee..eeeee..........hhhhhhhhh...eeeehhhhhh......eeeeeee........ee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------N-------------------------M---------Q------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------ETF_BETA             ------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1        Exon 1.2b  PDB: B:20-72 UniProt: 20-72               Exon 1.3  PDB: B:73-125 UniProt: 73-125              Exon 1.4             Exon 1.5  PDB: B:147-199 UniProt: 147-199            Exon 1.6  PDB: B:200-255 UniProt: 200-255                Transcript 1
                 2a1u B   4 LRVLVAVKRVIDYAVKIRVKPDRTGVVTDGVKHSMNPFCEIAVEEAVRLKEKKLVKEVIAVSCGPAQCQETIRTALAMGADRGIHVEVPPAEAERLGPLQVARVLAKLAEKEKVDLVLLGKQAIDDDCNQTGQMTAGFLDWPQGTFASQVTLEGDKLKVERAIDGGLETLRLKLPAVVTADLRLNEPRYATLPNIMKAKKKKIEVIKPGDLGVDLTSKLSVISVEDPPQRTAGVKVETTEDLVAKLKEIGRI 255
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: TPP-binding domain (120)

Human (Homo sapiens) (9)

2a1uA02

A:205-333

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Human (Homo sapiens) (27)

2a	2a1uA01	A:19-204
2b	2a1uB00	B:4-255

(no "Pfam Domain" information available for 2A1U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ETFA_HUMAN | P13804)

molecular function
	GO:0003995	acyl-CoA dehydrogenase activity	Catalysis of the reaction: acyl-CoA + acceptor = 2,3-dehydroacyl-CoA + reduced acceptor.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0000062	fatty-acyl-CoA binding	Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0052890	oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a flavin.
biological process
	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	GO:0055088	lipid homeostasis	Any process involved in the maintenance of an internal steady state of lipid within an organism or cell.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	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.

Chain B (ETFB_HUMAN | P38117)

molecular function
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
biological process
	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	A fatty acid beta-oxidation pathway in which the initial step of each oxidation cycle, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA dehydrogenase; the electrons removed by oxidation pass through the respiratory chain to oxygen and leave H2O as the product. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0022904	respiratory electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	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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	2a1u
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	ETFB_HUMAN \| P38117
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	231680
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UniProtKB/Swiss-Prot
	ETFA_HUMAN \| P13804	:	1efv 1t9g 2a1t
	ETFB_HUMAN \| P38117	:	1efv 1t9g 2a1t

1efv	WILD TYPE STRUCTURE
1t9g	WILD TYPE COMPLEX WITH MCAD
2a1t	E165BETAA MUTANT WITH MCAD

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (7, 7)

PROSITE Motifs (2, 2)

Exons (6, 6)

Sequences/Alignments

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SCOP Domains (2, 3)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (14, 21)

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