2O23 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Title :   THE STRUCTURE OF WILD-TYPE HUMAN HADH2 (17BETA-HYDROXYSTEROID DEHYDROGENASE TYPE 10) BOUND TO NAD+ AT 1.2 A

Authors :   K. L. Kavanagh, N. Shafqat, K. Scholer, J. Debreczeni, J. Zschocke, F. V J. Weigelt, C. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann, St Genomics Consortium (Sgc)

Date :   29 Nov 06 (Deposition) - 12 Dec 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

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

Keywords :   Hsd17B10, Schad, Erab, Type Ii Hadh, 2-Methyl-3-Hydroxybutyryl-Coa Dehydrogenase, Mhbd, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. L. Kavanagh, N. Shafqat, K. Scholer, J. Debreczeni, J. Zschocke, F. Von Delft, J. Weigelt, C. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann
The Structure Of Wild-Type Human Hadh2 (17Beta-Hydroxysteroid Dehydrogenase Type 10) Bound To Nad+ At 1. 2 A
To Be Published
PubMed: search

Molecule 1 - HADH2 PROTEIN
	Chains	:	A, B
	EC Number	:	1.1.1.178
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11-DERIVATIVE
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	HADH2
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	HYDROXYACYL-COENZYME A DEHYDROGENASE, TYPE II

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:17 , SER A:20 , GLY A:21 , LEU A:22 , ASP A:41 , LEU A:42 , ALA A:63 , ASP A:64 , VAL A:65 , CYS A:91 , ALA A:92 , VAL A:120 , THR A:153 , ALA A:154 , TYR A:168 , LYS A:172 , PRO A:198 , GLY A:199 , PHE A:201 , THR A:203 , PRO A:204 , HOH A:806 , HOH A:844 , HOH A:851 , HOH A:859 , HOH A:928 , HOH A:939 , HOH A:964 , HOH A:995	BINDING SITE FOR RESIDUE NAD A 802
2	AC2	SOFTWARE	GLY B:17 , SER B:20 , GLY B:21 , LEU B:22 , ASP B:41 , LEU B:42 , ALA B:63 , ASP B:64 , VAL B:65 , CYS B:91 , ALA B:92 , GLY B:93 , VAL B:120 , THR B:153 , ALA B:154 , TYR B:168 , LYS B:172 , PRO B:198 , GLY B:199 , LEU B:200 , PHE B:201 , THR B:203 , PRO B:204 , LEU B:205 , HOH B:806 , HOH B:845 , HOH B:848 , HOH B:867 , HOH B:886 , HOH B:913 , HOH B:1035	BINDING SITE FOR RESIDUE NAD B 803
3	AC3	SOFTWARE	GLU A:249 , VAL A:250 , ARG A:252 , GLU B:249 , VAL B:250 , ARG B:252 , HOH B:884 , HOH B:900 , HOH B:1090	BINDING SITE FOR RESIDUE GOL B 801

(no "SS Bond" information available for 2O23)

Asymmetric Unit

No.	Residues
1	Phe A:223	-	Pro A:224
2	Phe B:223	-	Pro B:224

Asymmetric Unit (3, 6)

								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/B	L	122	V
2	UniProt	VAR_015988	R	130	C	HCD2_HUMAN	Disease (MHBD deficiency)	28935475	A/B	R	130	C
3	UniProt	VAR_032093	N	247	S	HCD2_HUMAN	Disease (MHBD deficiency)	122461163	A/B	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/B	L	122	V
2	UniProt	VAR_015988	R	130	C	HCD2_HUMAN	Disease (MHBD deficiency)	28935475	A/B	R	130	C
3	UniProt	VAR_032093	N	247	S	HCD2_HUMAN	Disease (MHBD deficiency)	122461163	A/B	N	247	S

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

Asymmetric Unit (1, 2)

	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	2	A:155-183 B: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 B:155-183

Asymmetric Unit (6, 12)

	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	2	A:6-9 B:1-9	4 9
1.2	ENST00000168216	2	ENSE00000846304	X:53460833-53460669	165	HCD2_HUMAN	10-64	55	2	A:10-64 B:10-64	55 55
1.3a	ENST00000168216	3a	ENSE00000671344	X:53459359-53459195	165	HCD2_HUMAN	65-119	55	2	A:65-119 B:65-119	55 55
1.4a	ENST00000168216	4a	ENSE00000671345	X:53459064-53458936	129	HCD2_HUMAN	120-162	43	2	A:120-162 B:120-162	43 43
1.5c	ENST00000168216	5c	ENSE00000671346	X:53458854-53458746	109	HCD2_HUMAN	163-199	37	2	A:163-199 B:163-199	37 37
1.6b	ENST00000168216	6b	ENSE00000846303	X:53458542-53458206	337	HCD2_HUMAN	199-261	63	2	A:199-261 (gaps) B:199-261 (gaps)	63 63

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:248
 aligned with HCD2_HUMAN | Q99714 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:258
                                                                                                                                                                                                                                                                                         261  
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255     |  
           HCD2_HUMAN     6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRLDGAIRMQP--   -
               SCOP domains d2o23a_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2o23A00 A:6-263 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee..........ee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......----------hhhhhh........hhhhhhhhhhhhhhh......eeee.......... 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 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:199-261 (gaps) UniProt: 199-261              -- Transcript 1 (2)
                 2o23 A   6 RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTP----------NFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRLDGAIRMQPGS 263
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195        |-       215       225       235       245       255        
                                                                                                                                                                                                                                204        215

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with HCD2_HUMAN | Q99714 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:263
                                                                                                                                                                                                                                                                                              261  
                                    10        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|  
           HCD2_HUMAN     1 MAAACRSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRLDGAIRMQP--   -
               SCOP domains d2o23b_ B: automated matches                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2o23B00 B:1-263 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) ----------adh_short-2o23B01 B:11-187                                                                                                                                                       ---------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------adh_short-2o23B02 B:11-187                                                                                                                                                       ---------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...........eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhh...eeee..........ee....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee........--------hhhhhh........hhhhhhhhhhhhhhh......eeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------V-------C--------------------------------------------------------------------------------------------------------------------S---------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:155-183    -------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1aExon 1.2  PDB: B:10-64 UniProt: 10-64                  Exon 1.3a  PDB: B:65-119 UniProt: 65-119               Exon 1.4a  PDB: B:120-162 UniProt: 120-162 Exon 1.5c  PDB: B:163-199            ---------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6b  PDB: B:199-261 (gaps) UniProt: 199-261              -- Transcript 1 (2)
                 2o23 B   1 MAAACRSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVMTIAPGLFGTPLL--------NFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIRLDGAIRMQPGS 263
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     |   -    |  220       230       240       250       260   
                                                                                                                                                                                                                                       206      215

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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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: automated matches (114)

Human (Homo sapiens) [TaxId: 9606] (8)

1a	d2o23a_	A:
1b	d2o23b_	B:

Asymmetric Unit

Classes(

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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)

1a	2o23A00	A:6-263
1b	2o23B00	B:1-263

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short (92)

Homo sapiens (Human) (21)

1a	adh_short-2o23B01	B:11-187
1b	adh_short-2o23B02	B:11-187

Asymmetric Unit(hide GO term definitions)

Chain A,B (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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	2o23
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	HCD2_HUMAN \| Q99714	:	1f67 1so8 1u7t

(no "Related Entries Specified in the PDB File" available for 2O23)

Description

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