1ZSY - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF HUMAN MITOCHONDRIAL 2-ENOYL THIOESTER REDUCTASE (CGI-63)

Authors :   P. Lukacik, N. Shafqat, K. L. Kavanagh, C. Johansson, C. Smee, A. Edward C. Arrowsmith, M. Sundstrom, F. Von Delft, U. Oppermann, Structural Consortium (Sgc)

Date :   25 May 05 (Deposition) - 07 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Medium-Chain Dehydrogenase/Reductase, Oxidoreductase, 2-Enoyl Thioester Reductase, Fatty Acid Synthesis (Type 2), Structural Genomics, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Lukacik, N. Shafqat, K. L. Kavanagh, C. Johansson, C. Smee, A. Edwards, C. Arrowsmith, M. Sundstrom, F. Von Delft, U. Oppermann
The Structure Of Human Mitochondrial 2-Enoyl Thioester Reductase (Cgi-63)
To Be Published
PubMed: search

Molecule 1 - MITOCHONDRIAL 2-ENOYL THIOESTER REDUCTASE
	Chains	:	A
	EC Number	:	1.3.1.38
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	MECR, NBRF1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HOMOLOG OF YEAST 2-ENOYL THIOESTER REDUCTASE
	Synonym	:	TRANS-2-ENOYL-COA REDUCTASE, HSNRBF-1, NRBF-1, CGI-63, NUCLEAR RECEPTOR-BINDING FACTOR 1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:175 , SER A:176 , ASN A:177 , SER A:178 , VAL A:199 , ARG A:200 , ARG A:202 , HOH A:581 , HOH A:724	BINDING SITE FOR RESIDUE SO4 A 500
2	AC2	SOFTWARE	PRO A:68 , ASN A:151 , SER A:178 , GLY A:179 , VAL A:180 , LYS A:352 , HOH A:548 , HOH A:564 , HOH A:772	BINDING SITE FOR RESIDUE GOL A 501
3	AC3	SOFTWARE	ASN A:17 , GLN A:166 , PRO A:167 , GLY A:168 , ASP A:169 , HOH A:640 , HOH A:757	BINDING SITE FOR RESIDUE GOL A 502
4	AC4	SOFTWARE	HIS A:34 , HIS A:35	BINDING SITE FOR RESIDUE GOL A 503

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

Asymmetric Unit

No.	Residues
1	Leu A:84	-	Pro A:85

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_027935	F	96	L	MECR_HUMAN	Polymorphism	1128400	A	L	80	L
2	UniProt	VAR_055486	R	227	K	MECR_HUMAN	Polymorphism	11544658	A	R	211	K
3	UniProt	VAR_077997	G	232	E	MECR_HUMAN	Disease (DYTOABG)	762913101	A	G	216	E
4	UniProt	VAR_055487	R	258	L	MECR_HUMAN	Polymorphism	34835902	A	R	242	L
5	UniProt	VAR_077998	R	258	W	MECR_HUMAN	Disease (DYTOABG)	145192716	A	R	242	W
6	UniProt	VAR_078000	Y	285	C	MECR_HUMAN	Disease (DYTOABG)	759218713	A	Y	269	C

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

Biological Unit 1 (6, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_027935	F	96	L	MECR_HUMAN	Polymorphism	1128400	A	L	80	L
2	UniProt	VAR_055486	R	227	K	MECR_HUMAN	Polymorphism	11544658	A	R	211	K
3	UniProt	VAR_077997	G	232	E	MECR_HUMAN	Disease (DYTOABG)	762913101	A	G	216	E
4	UniProt	VAR_055487	R	258	L	MECR_HUMAN	Polymorphism	34835902	A	R	242	L
5	UniProt	VAR_077998	R	258	W	MECR_HUMAN	Disease (DYTOABG)	145192716	A	R	242	W
6	UniProt	VAR_078000	Y	285	C	MECR_HUMAN	Disease (DYTOABG)	759218713	A	Y	269	C

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

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

Asymmetric Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000263702	1b	ENSE00001897993	chr1:29557444-29557243	202	MECR_HUMAN	1-59	59	1	A:11-43	33
1.7c	ENST00000263702	7c	ENSE00001694933	chr1:29543197-29543100	98	MECR_HUMAN	59-92	34	1	A:43-76	34
1.8c	ENST00000263702	8c	ENSE00000956360	chr1:29542648-29542517	132	MECR_HUMAN	92-136	45	1	A:76-120	45
1.9c	ENST00000263702	9c	ENSE00001065053	chr1:29533417-29533274	144	MECR_HUMAN	136-184	49	1	A:120-168	49
1.10d	ENST00000263702	10d	ENSE00000956362	chr1:29529745-29529643	103	MECR_HUMAN	184-218	35	1	A:168-202	35
1.11b	ENST00000263702	11b	ENSE00000956363	chr1:29528557-29528455	103	MECR_HUMAN	218-252	35	1	A:202-236	35
1.13a	ENST00000263702	13a	ENSE00001757446	chr1:29527101-29527028	74	MECR_HUMAN	253-277	25	1	A:237-261	25
1.14a	ENST00000263702	14a	ENSE00001681965	chr1:29522770-29522710	61	MECR_HUMAN	277-297	21	1	A:261-281	21
1.14f	ENST00000263702	14f	ENSE00001694907	chr1:29522525-29522453	73	MECR_HUMAN	298-322	25	1	A:282-306	25
1.15d	ENST00000263702	15d	ENSE00001829391	chr1:29520691-29520329	363	MECR_HUMAN	322-373	52	1	A:306-357	52

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:347
 aligned with MECR_HUMAN | Q9BV79 from UniProtKB/Swiss-Prot  Length:373

    Alignment length:347
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       
           MECR_HUMAN    27 HGPAASSYSASAEPARVRALVYGHHGDPAKVVELKNLELAAVRGSDVRVKMLAAPINPSDINMIQGNYGFLPELPAVGGNEGVAQVVAVGSNVTGLKPGDWVIPANAGLGTWRTEAVFSEEALIQVPSDIPLQSAATLGVNPCTAYRMLMDFEQLQPGDSVIQNASNSGVGQAVIQIAAALGLRTINVVRDRPDIQKLSDRLKSLGAEHVITEEELRRPEMKNFFKDMPQPRLALNCVGGKSSTELLRQLARGGTMVTYGGMAKQPVVASVSLLIFKDLKLRGFWLSQWKKDHSPDQFKELILTLCDLIRRGQLTAPACSQVPLQDYQSALEASMKPFISSKQILTM 373
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------1zsyA02 A:149-325 NAD(P)-binding Rossmann-like Domain                                                                                                                            -------------------------------- CATH domains
               Pfam domains -------------------------------------------ADH_N-1zsyA01 A:54-127                                                    ---------------------------------------------------ADH_zinc_N-1zsyA02 A:179-315                                                                                                             ------------------------------------------ Pfam domains
         Sec.struct. author ................eeeeee....hhhhheeeeee........eeeeeeeeee.hhhhhhhhhh.........ee.....eeeeeee...........eeee..........eeeee...eeee....hhhhhhhh.hhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh...eeeehhhhhhhhhhhh........eeee..hhhhhhhhhh......eeee...........hhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee..hhhhhhhhhh......eeeee. Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------L----------------------------------------------------------------------------------------------------------------------------------K----E-------------------------L--------------------------C---------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:11-43          --------------------------------Exon 1.8c  PDB: A:76-120 UniProt: 92-136     -----------------------------------------------Exon 1.10d  PDB: A:168-202         ----------------------------------Exon 1.13a  PDB: A:237-26--------------------Exon 1.14f  PDB: A:282-30--------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.7c  PDB: A:43-76           -------------------------------------------Exon 1.9c  PDB: A:120-168 UniProt: 136-184       ---------------------------------Exon 1.11b  PDB: A:202-236         ------------------------Exon 1.14a           ------------------------Exon 1.15d  PDB: A:306-357 UniProt: 322-373          Transcript 1 (2)
                 1zsy A  11 VDLGTENLYFQSMPARVRALVYGHHGDPAKVVELKNLELAAVRGSDVRVKMLAAPINPSDINMIQGNYGLLPELPAVGGNEGVAQVVAVGSNVTGLKPGDWVIPANAGLGTWRTEAVFSEEALIQVPSDIPLQSAATLGVNPCTAYRMLMDFEQLQPGDSVIQNASNSGVGQAVIQIAAALGLRTINVVRDRPDIQKLSDRLKSLGAEHVITEEELRRPEMKNFFKDMPQPRLALNCVGGKSSTELLRQLARGGTMVTYGGMAKQPVVASVSLLIFKDLKLRGFWLSQWKKDHSPDQFKELILTLCDLIRRGQLTAPACSQVPLQDYQSALEASMKPFISSKQILTM 357
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

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 1ZSY)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Human (Homo sapiens) (188)

1zsyA02

A:149-325

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GroES (70)

Family: ADH_N (62)

Homo sapiens (Human) (18)

ADH_N-1zsyA01

A:54-127

Clan: NADP_Rossmann (1239)

Family: ADH_zinc_N (75)

Homo sapiens (Human) (24)

ADH_zinc_N-1zsyA02

A:179-315

Asymmetric Unit(hide GO term definitions)

Chain A (MECR_HUMAN | Q9BV79)

molecular function
	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:0019166	trans-2-enoyl-CoA reductase (NADPH) activity	Catalysis of the reaction: acyl-CoA + NADP+ = trans-2,3-dehydroacyl-CoA + NADPH + H+.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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		Leu A:84 - Pro A:85	[ RasMol ]

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	1zsy
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	MECR_HUMAN \| Q9BV79	:	2vcy

(no "Related Entries Specified in the PDB File" available for 1ZSY)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

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Exons (10, 10)

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