1SO8 - JenaLib

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Title :   ABETA-BOUND HUMAN ABAD STRUCTURE [ALSO KNOWN AS 3-HYDROXYACYL-COA DEHYDROGENASE TYPE II (TYPE II HADH), ENDOPLASMIC RETICULUM-ASSOCIATED AMYLOID BETA-PEPTIDE BINDING PROTEIN (ERAB)]

Authors :   J. W. Lustbader, M. Cirilli, H. Wu

Date :   13 Mar 04 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (8x)

Keywords :   Alcohol Dehydrogenase; Rossmann Fold; Abeta-Induced Distorsion, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. W. Lustbader, M. Cirilli, C. Lin, H. W. Xu, K. Takuma, N. Wang, C. Caspersen, X. Chen, S. Pollak, M. Chaney, F. Trinchese, F. Gunn-Moore, L. F. Lue, D. G. Walker, P. Kuppusamy, Z. L. Zewier, O. Arancio, D. Stern, S. S. Yan, H. Wu
Abad Directly Links Abeta To Mitochondrial Toxicity In Alzheimer'S Disease.
Science V. 304 448 2004
PubMed-ID: 15087549 | Reference-DOI: 10.1126/SCIENCE.1091230

Molecule 1 - 3-HYDROXYACYL-COA DEHYDROGENASE TYPE II
	Chains	:	A
	EC Number	:	1.1.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PGE5
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	HADH2, ERAB, XH98G2, SCHAD
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	TYPE II HADH, ENDOPLASMIC RETICULUM-ASSOCIATED AMYLOID BETA- PEPTIDE BINDING PROTEIN (ERAB), SHORT-CHAIN TYPE DEHYDROGENASE/REDUCTASE XH98G2

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A
Biological Unit 2 (8x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:67 , GLU A:68 , LYS A:69	BINDING SITE FOR RESIDUE NA A 301
2	AC2	SOFTWARE	GLY A:17 , SER A:20 , HOH A:522 , HOH A:545 , HOH A:560 , HOH A:602	BINDING SITE FOR RESIDUE NA A 302
3	AC3	SOFTWARE	ALA A:154 , SER A:155 , GLY A:173 , ILE A:175 , VAL A:176 , HOH A:570	BINDING SITE FOR RESIDUE CL A 303

(no "SS Bond" information available for 1SO8)

(no "Cis Peptide Bond" information available for 1SO8)

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015987	L	122	V	HCD2_HUMAN	Disease (MHBD deficiency)	28935476	A	L	122	V
2	UniProt	VAR_015988	R	130	C	HCD2_HUMAN	Disease (MHBD deficiency)	28935475	A	R	130	C
3	UniProt	VAR_032093	N	247	S	HCD2_HUMAN	Disease (MHBD deficiency)	122461163	A	N	247	S

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

Biological Unit 1 (3, 12)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015987	L	122	V	HCD2_HUMAN	Disease (MHBD deficiency)	28935476	A	L	122	V
2	UniProt	VAR_015988	R	130	C	HCD2_HUMAN	Disease (MHBD deficiency)	28935475	A	R	130	C
3	UniProt	VAR_032093	N	247	S	HCD2_HUMAN	Disease (MHBD deficiency)	122461163	A	N	247	S

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

Biological Unit 2 (3, 24)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015987	L	122	V	HCD2_HUMAN	Disease (MHBD deficiency)	28935476	A	L	122	V
2	UniProt	VAR_015988	R	130	C	HCD2_HUMAN	Disease (MHBD deficiency)	28935475	A	R	130	C
3	UniProt	VAR_032093	N	247	S	HCD2_HUMAN	Disease (MHBD deficiency)	122461163	A	N	247	S

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HCD2_HUMAN	155-183	1	A:155-183

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HCD2_HUMAN	155-183	4	A:155-183

Biological Unit 2 (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HCD2_HUMAN	155-183	8	A:155-183

Asymmetric Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000168216	1a	ENSE00001038851	X:53461320-53461266	55	HCD2_HUMAN	1-9	9	1	A:6-9	4
1.2	ENST00000168216	2	ENSE00000846304	X:53460833-53460669	165	HCD2_HUMAN	10-64	55	1	A:10-64	55
1.3a	ENST00000168216	3a	ENSE00000671344	X:53459359-53459195	165	HCD2_HUMAN	65-119	55	1	A:65-119 (gaps)	55
1.4a	ENST00000168216	4a	ENSE00000671345	X:53459064-53458936	129	HCD2_HUMAN	120-162	43	1	A:120-162	43
1.5c	ENST00000168216	5c	ENSE00000671346	X:53458854-53458746	109	HCD2_HUMAN	163-199	37	1	A:163-199	37
1.6b	ENST00000168216	6b	ENSE00000846303	X:53458542-53458206	337	HCD2_HUMAN	199-261	63	1	A:199-253 (gaps)	55

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:208
 aligned with HCD2_HUMAN | Q99714 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:248
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245        
           HCD2_HUMAN     6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRL 253
               SCOP domains d1so8a_ A: Type II 3-hydroxyacyl-CoA dehydrogenase                                                                                                                                                                                                       SCOP domains
               CATH domains 1so8A00 A:6-253 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                      CATH domains
               Pfam domains -----adh_short-1so8A01 A:11-187                                                                                                                                                       --------------------                     ------------------------- Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eee.....-------------------.....hhhhhhhhhhhhhhhhhhhh.........eeeeee..........hhhhhh...hhhhhhhhhhhhhhh...eeeeeee..........---------------------hhhhhhhhhhhhhhh......eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------V-------C--------------------------------------------------------------------------------------------------------------------S------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:155-183    ---------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1aExon 1.2  PDB: A:10-64 UniProt: 10-64                  Exon 1.3a  PDB: A:65-119 (gaps) UniProt: 65-119        Exon 1.4a  PDB: A:120-162 UniProt: 120-162 Exon 1.5c  PDB: A:163-199            ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6b  PDB: A:199-253 (gaps) UniProt: 199-261       Transcript 1 (2)
                 1so8 A   6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGI-------------------FQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLT---------------------DPAEYAHLVQAIIENPFLNGEVIRL 253
                                    15        25        35        45        55        65        75        85        |-         -       115       125       135       145       155       165       175       185       195       205 |       -         -   |   235       245        
                                                                                                                   94                 114                                                                                          207                   229

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Type II 3-hydroxyacyl-CoA dehydrogenase (6)

Human (Homo sapiens) [TaxId: 9606] (2)

d1so8a_

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)

1so8A00

A:6-253

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Homo sapiens (Human) (21)

adh_short-1so8A01

A:11-187

Asymmetric Unit(hide GO term definitions)

Chain A (HCD2_HUMAN | Q99714)

molecular function
	GO:0047015	3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity	Catalysis of the reaction: NAD+ + 2-methyl-3-hydroxybutyryl-CoA = NADH + H+ + 2-methylaceto-acetyl-CoA.
	GO:0003857	3-hydroxyacyl-CoA dehydrogenase activity	Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0018454	acetoacetyl-CoA reductase activity	Catalysis of the reaction: (R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH + H+.
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	GO:0008709	cholate 7-alpha-dehydrogenase activity	Catalysis of the reaction: cholate + NAD(+) = 3alpha,12alpha-dihydroxy-7-oxo-5beta-cholanate + H(+) + NADH.
	GO:0004303	estradiol 17-beta-dehydrogenase activity	Catalysis of the reaction: estradiol-17-beta + NADP+ = estrone + NADPH + H+.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen receptor.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005496	steroid binding	Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
	GO:0030283	testosterone dehydrogenase [NAD(P)] activity	Catalysis of the reaction: testosterone + NAD(P)+ = androst-4-ene-3,17-dione + NAD(P)H + H+.
biological process
	GO:0033327	Leydig cell differentiation	The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
	GO:0009083	branched-chain amino acid catabolic process	The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
	GO:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	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:0070901	mitochondrial tRNA methylation	The posttranscriptional addition of methyl groups to specific residues in a mitochondrial tRNA molecule.
	GO:0090646	mitochondrial tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group, in the mitochondrion.
	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:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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