1M76 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE S137C MUTANT OF L-3-HYDROXYACYL-COA DEHYDROGENASE IN COMPLEX WITH NAD AND ACETOACETYL-COA

Authors :   J. J. Barycki, L. J. Banaszak

Date :   18 Jul 02 (Deposition) - 03 Feb 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Rossmann Fold, Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Barycki, L. J. Banaszak
Crystal Structure Of The S137C Mutant Of L-3-Hydroxyacyl-Coa Dehydrogenase In Complex With Nad And Acetoacetyl-Coa
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - 3-HYDROXYACYL-COA DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SHORT CHAIN
	Gene	:	HCDH
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	L-3-HYDROXYACYL-COA DEHYDROGENASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CAA	2	Ligand/Ion	ACETOACETYL-COENZYME A
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:61 , CYS A:137 , PHE A:160 , ASN A:161 , PRO A:164 , VAL A:165 , MET A:166 , ASN A:208 , LEU A:211 , PRO A:243 , MET A:244 , LEU A:249 , TYR A:252 , NAD A:350 , HOH A:801 , HOH A:911 , HOH A:1028 , HOH A:1040 , HOH A:1147 , GLY B:239 , ALA B:240	BINDING SITE FOR RESIDUE CAA A 351
2	AC2	SOFTWARE	GLY A:239 , ALA A:240 , HOH A:802 , SER B:61 , VAL B:65 , LYS B:68 , HIS B:158 , PHE B:160 , ASN B:161 , PRO B:164 , VAL B:165 , MET B:166 , ASN B:208 , LEU B:211 , PRO B:243 , MET B:244 , LEU B:249 , TYR B:252 , NAD B:750 , HOH B:1100 , HOH B:1242 , HOH B:1252	BINDING SITE FOR RESIDUE CAA B 751
3	AC3	SOFTWARE	ILE A:21 , GLY A:24 , LEU A:25 , MET A:26 , ASP A:45 , GLN A:46 , ALA A:107 , ILE A:108 , GLU A:110 , LYS A:115 , ASN A:135 , CYS A:137 , HIS A:158 , PHE A:159 , ASN A:161 , VAL A:253 , THR A:257 , LYS A:293 , CAA A:351 , HOH A:804 , HOH A:863 , HOH A:878 , HOH A:1017 , HOH A:1020 , HOH A:1024 , HOH A:1146	BINDING SITE FOR RESIDUE NAD A 350
4	AC4	SOFTWARE	GLY B:24 , LEU B:25 , MET B:26 , ASP B:45 , GLN B:46 , ALA B:107 , ILE B:108 , GLU B:110 , LYS B:115 , ASN B:135 , CYS B:137 , HIS B:158 , PHE B:159 , ASN B:161 , VAL B:253 , LYS B:293 , CAA B:751 , HOH B:832 , HOH B:841 , HOH B:853 , HOH B:1021 , HOH B:1030 , HOH B:1038 , HOH B:1145	BINDING SITE FOR RESIDUE NAD B 750

(no "SS Bond" information available for 1M76)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:161	-	Pro A:162
2	Asn B:161	-	Pro B:162

Asymmetric/Biological Unit (5, 10)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_024079	A	40	T	HCDH_HUMAN	Disease (HADH deficiency)	137853101	A/B	A	28	T
2	UniProt	VAR_024080	D	57	E	HCDH_HUMAN	Disease (HADH deficiency)	137853102	A/B	D	45	E
3	UniProt	VAR_026764	L	86	P	HCDH_HUMAN	Polymorphism	4956145	A/B	P	74	P
4	UniProt	VAR_055701	Q	152	H	HCDH_HUMAN	Polymorphism	1051519	A/B	Q	140	H
5	UniProt	VAR_024081	P	258	L	HCDH_HUMAN	Disease (HHF4)	137853103	A/B	P	246	L

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	3HCDH	PS00067	3-hydroxyacyl-CoA dehydrogenase signature.	HCDH_HUMAN	213-237	2	A:201-225 B:201-225

Asymmetric/Biological Unit (8, 16)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000309522	1c	ENSE00001196027	chr4:108910940-108911220	281	HCDH_HUMAN	1-44	44	2	A:12-32 B:12-32	21 21
1.4	ENST00000309522	4	ENSE00000333879	chr4:108930915-108931043	129	HCDH_HUMAN	45-87	43	2	A:33-75 B:33-75	43 43
1.5a	ENST00000309522	5a	ENSE00000841666	chr4:108935587-108935744	158	HCDH_HUMAN	88-140	53	2	A:76-128 B:76-128	53 53
1.6	ENST00000309522	6	ENSE00000841667	chr4:108940696-108940822	127	HCDH_HUMAN	140-182	43	2	A:128-170 B:128-170	43 43
1.7	ENST00000309522	7	ENSE00000841668	chr4:108944630-108944719	90	HCDH_HUMAN	183-212	30	2	A:171-200 B:171-200	30 30
1.8b	ENST00000309522	8b	ENSE00000841669	chr4:108948844-108948916	73	HCDH_HUMAN	213-237	25	2	A:201-225 B:201-225	25 25
1.10b	ENST00000309522	10b	ENSE00000841670	chr4:108954332-108954448	117	HCDH_HUMAN	237-276	40	2	A:225-264 B:225-264	40 40
1.11d	ENST00000309522	11d	ENSE00001561694	chr4:108955395-108956331	937	HCDH_HUMAN	276-314	39	2	A:264-302 B:264-302	39 39

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:291
 aligned with HCDH_HUMAN | Q16836 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:291
                                    33        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 
           HCDH_HUMAN    24 KIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENLKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains d1m76a2 A:12-203 Short chain L-3-hydroxyacyl CoA dehydrogenase                                                                                                                                  d1m76a1 A:204-302 Short chain L-3-hydroxyacyl CoA dehydrogenase                                     SCOP domains
               CATH domains 1m76A01 A:12-207 NAD(P)-binding Rossmann-like Domain                                                                                                                                                ---1m76A02 A:211-297 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2            ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeee.hhhhhhhhh.eeee....hhhhhhhhhhhhh.......eeee.....hhhhhhh...hhh.eeeeee........eeeee.....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------T----------------E----------------------------P-----------------------------------------------------------------H---------------------------------------------------------------------------------------------------------L-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: A:201-225    ----------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c            Exon 1.4  PDB: A:33-75 UniProt: 45-87      Exon 1.5a  PDB: A:76-128 UniProt: 88-140             ------------------------------------------Exon 1.7  PDB: A:171-200      ------------------------Exon 1.10b  PDB: A:225-264              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:128-170 UniProt: 140-182  ------------------------------Exon 1.8b  PDB: A:201-225--------------------------------------Exon 1.11d  PDB: A:264-302              Transcript 1 (2)
                 1m76 A  12 KIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTCSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 302
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with HCDH_HUMAN | Q16836 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:291
                                    33        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 
           HCDH_HUMAN    24 KIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENLKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains d1m76b2 B:12-203 Short chain L-3-hydroxyacyl CoA dehydrogenase                                                                                                                                  d1m76b1 B:204-302 Short chain L-3-hydroxyacyl CoA dehydrogenase                                     SCOP domains
               CATH domains 1m76B01 B:12-207 NAD(P)-binding Rossmann-like Domain                                                                                                                                                ---1m76B02 B:211-297 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2            ----- CATH domains
           Pfam domains (1) -----3HCDH_N-1m76B03 B:17-202                                                                                                                                                                  -3HCDH-1m76B01 B:204-301                                                                           - Pfam domains (1)
           Pfam domains (2) -----3HCDH_N-1m76B04 B:17-202                                                                                                                                                                  -3HCDH-1m76B02 B:204-301                                                                           - Pfam domains (2)
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeee.hhhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhh...hhh.eeeeee........eeeee.....hhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------T----------------E----------------------------P-----------------------------------------------------------------H---------------------------------------------------------------------------------------------------------L-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: B:201-225    ----------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c            Exon 1.4  PDB: B:33-75 UniProt: 45-87      Exon 1.5a  PDB: B:76-128 UniProt: 88-140             ------------------------------------------Exon 1.7  PDB: B:171-200      ------------------------Exon 1.10b  PDB: B:225-264              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: B:128-170 UniProt: 140-182  ------------------------------Exon 1.8b  PDB: B:201-225--------------------------------------Exon 1.11d  PDB: B:264-302              Transcript 1 (2)
                 1m76 B  12 KIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTCSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 302
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301

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

Human (Homo sapiens) (188)

1a	1m76A01	A:12-207
1b	1m76B01	B:12-207

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (60)

Homologous Superfamily: N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 (59)

Human (Homo sapiens) (12)

2a	1m76A02	A:211-297
2b	1m76B02	B:211-297

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: 6PGD_C (47)

Family: 3HCDH (12)

Homo sapiens (Human) (4)

1a	3HCDH-1m76B01	B:204-301
1b	3HCDH-1m76B02	B:204-301

Clan: NADP_Rossmann (1239)

Family: 3HCDH_N (12)

Homo sapiens (Human) (4)

2a	3HCDH_N-1m76B03	B:17-202
2b	3HCDH_N-1m76B04	B:17-202

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HCDH_HUMAN | Q16836)

molecular function
	GO:0003857	3-hydroxyacyl-CoA dehydrogenase activity	Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
	GO:0070403	NAD+ binding	Interacting selectively and non-covalently with the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.
	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.
biological process
	GO:0006635	fatty acid beta-oxidation	A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
	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:0046676	negative regulation of insulin secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin.
	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:0014823	response to activity	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an activity stimulus.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0009725	response to hormone	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus.
	GO:0032868	response to insulin	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	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:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	1m76
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	HCDH_HUMAN \| Q16836
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	1.1.1.35
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	231530
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	609975
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	HCDH_HUMAN \| Q16836
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UniProtKB/Swiss-Prot
	HCDH_HUMAN \| Q16836	:	1f0y 1f12 1f14 1f17 1il0 1lsj 1lso 1m75 2hdh 3had 3rqs

1f0y	1F0Y IS A COMPARABLE WILD-TYPE STRUCTURE
1m75	1M75 IS THE CRYSTAL STRUCTURE OF THE N208S MUTANT OF L-3- HYDROXYACYL-COA DEHYDROGENASE IN COMPLEX WITH NAD AND ACETOACETYL-COA

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 10)

PROSITE Motifs (1, 2)

Exons (8, 16)

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SCOP Domains (2, 4)

CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (17, 17)

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