3HDH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PIG HEART SHORT CHAIN L-3-HYDROXYACYL COA DEHYDROGENASE REVISITED: SEQUENCE ANALYSIS AND CRYSTAL STRUCTURE DETERMINATION

Authors :   J. J. Barycki, L. K. O'Brien, J. J. Birktoft, A. W. Strauss, L. J. Banaszak

Date :   13 Apr 99 (Deposition) - 08 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidoreductase, Beta Oxidation, Schad, Catalytic Activity: L-3-Hydroxyacyl-Coa + Nad(+) = 3-Oxoacyl-Coa + Nadh (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Barycki, L. K. O'Brien, J. J. Birktoft, A. W. Strauss, L. J. Banaszak
Pig Heart Short Chain L-3-Hydroxyacyl-Coa Dehydrogenase Revisited: Sequence Analysis And Crystal Structure Determination.
Protein Sci. V. 8 2010 1999
PubMed-ID: 10548046
(for further references see the PDB file header)

Molecule 1 - PROTEIN (L-3-HYDROXYACYL COA DEHYDROGENASE)
	Chains	:	A, B, C
	EC Number	:	1.1.1.35
	Organ	:	HEART
	Organelle	:	MITOCHONDRIAL
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	SCHAD

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NAD	3	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:25 , MET A:26 , ASP A:45 , GLN A:46 , ALA A:107 , ILE A:108 , VAL A:109 , GLU A:110 , VAL A:114 , LYS A:115 , ASN A:135 , SER A:137 , HIS A:158 , PHE A:159	BINDING SITE FOR RESIDUE NAD A 350
2	AC2	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 , SER B:137 , PHE B:159	BINDING SITE FOR RESIDUE NAD B 750
3	AC3	SOFTWARE	GLY C:22 , LEU C:25 , MET C:26 , ASP C:45 , GLN C:46 , ALA C:107 , ILE C:108 , GLU C:110 , LYS C:115 , LEU C:118 , ASN C:135 , THR C:136 , SER C:137 , HIS C:158 , PHE C:159 , ASN C:161	BINDING SITE FOR RESIDUE NAD C 1150

(no "SS Bond" information available for 3HDH)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3HDH)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	3HCDH	PS00067	3-hydroxyacyl-CoA dehydrogenase signature.	HCDH_PIG	213-237	3	A:201-225 B:201-225 C:201-223

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	3HCDH	PS00067	3-hydroxyacyl-CoA dehydrogenase signature.	HCDH_PIG	213-237	2	- - C:201-223

(no "Exon" information available for 3HDH)

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:291
 aligned with HCDH_PIG | P00348 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_PIG    24 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains d3hdha2 A:12-203 Short chain L-3-hydroxyacyl CoA dehydrogenase                                                                                                                                  d3hdha1 A:204-302 Short chain L-3-hydroxyacyl CoA dehydrogenase                                     SCOP domains
               CATH domains 3hdhA01 A:12-207 NAD(P)-binding Rossmann-like Domain                                                                                                                                                ---3hdhA02 A:211-297 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2            ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhheeee..hhh......eeee.....hhhhhhhhhhhhhh.....eeee......hhhhhhh...hhheeeeee........eeeeee.....hhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhh...hhh...hhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: A:201-225    ----------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdh A  12 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTGEGFYKYK 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_PIG | P00348 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_PIG    24 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains d3hdhb2 B:12-203 Short chain L-3-hydroxyacyl CoA dehydrogenase                                                                                                                                  d3hdhb1 B:204-302 Short chain L-3-hydroxyacyl CoA dehydrogenase                                     SCOP domains
               CATH domains 3hdhB01 B:12-207 NAD(P)-binding Rossmann-like Domain                                                                                                                                                ---3hdhB02 B:211-297 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2            ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee...hhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh...............hhhhhhh.eeee...........eeee.....hhhhhhhhhhhhhh.....eeee......hhhhhhh...hhheeeeee........eeeee......hhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhhhhhh.........hhhhhhhhh....hhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: B:201-225    ----------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdh B  12 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTGEGFYKYK 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 C from PDB  Type:PROTEIN  Length:265
 aligned with HCDH_PIG | P00348 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:284
                                    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    
             HCDH_PIG    24 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIIDGWHEMDSQNPLFQPSPAMNKLVAENKFGKKTG 307
               SCOP domains d3hdhc2 C:12-203 Short chain L-3-hydroxyacyl CoA dehydrogenase                                                                                                                                  d3hdhc1 C:204-295 Sh     ort chain L-    3-hydroxyacyl CoA dehyd          rogenase           SCOP domains
               CATH domains 3hdhC01 C:12-207 NAD(P)-binding Rossmann-like Domain                                                                                                                                                ---3hdhC02 C:211     -292 N-(1-d-    carboxylethyl)-l-norval          ine Dehydrogena--- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhheeee..hhh......eeee.....hhhhhhhhhhhhhh.....eeee......hhhhhhh...hhh.eeee.........eeeeee.....hhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhh.-----..hhhhhhhhh.----.hhhhhhhh......hhhhhh..----------.................. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: C:201-223    ---------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdh C  12 KILVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSSISTSTDAASVVHSTDLVVEAIVENLKVKSELFKRLDKFAAEHTIFASNTSSLQITSLANATTRQDRFAGLHFFNPVPLMKLVEVVKTPMTSQKTLESLVDFSKTLGKHPVSCKDTPGFIVNRLLVPYLIEAVRLYE-----KEDIDTAMKLGA----GPFELLDYVGLDTTKFIIDGWHE----------SPAMNKLVAENKFGKKTG 295
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221 |     231        |-   |   251       261     |   -      |281       291    
                                                                                                                                                                                                                                             223   229        240  245                   267        278

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(

)

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)

Pig (Sus scrofa) (21)

1a	3hdhA01	A:12-207
1b	3hdhB01	B:12-207
1c	3hdhC01	C: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)

Pig (Sus scrofa) (1)

2a	3hdhA02	A:211-297
2b	3hdhB02	B:211-297
2c	3hdhC02	C:211-292

(no "Pfam Domain" information available for 3HDH)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (HCDH_PIG | P00348)

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: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: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.

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	Cis Peptide Bonds
		Asn A:161 - Pro A:162	[ RasMol ]
		Asn B:161 - Pro B:162	[ RasMol ]
		Asn C:161 - Pro C:162	[ RasMol ]

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	3hdh
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Description

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