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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN L-3- HYDROXYACYL-COA DEHYDROGENASE (EC1.1.1.35) FROM MITOCHONDRIA AT THE RESOLUTION 2.0 A, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR487, MITOCHONDRIAL PROTEIN PARTNERSHIP
 
Authors :  A. Kuzin, M. Su, J. Seetharaman, P. Patel, R. Xiao, C. Ciccosanti, R. Sha J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J Northeast Structural Genomics Consortium (Nesg), Mitochondri Protein Partnership (Mpp)
Date :  28 Apr 11  (Deposition) - 25 May 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Oxidoreductase, Mitochondrial Protein Partnership, Mpp (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Kuzin, M. Su, J. Seetharaman, P. Patel, R. Xiao, C. Ciccosanti, R. Shastry, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, L. Tong, J. F. Hunt
Northeast Structural Genomics Consortium Target Hr487
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROXYACYL-COENZYME A DEHYDROGENASE, MITOCHONDRIAL
    ChainsA, B
    EC Number1.1.1.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneHADH, HAD, HADHSC, SCHAD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHCDH, MEDIUM AND SHORT-CHAIN L-3-HYDROXYACYL-COENZYME A DEHYDROGENASE, SHORT-CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:220 , VAL A:224 , VAL A:265 , THR A:269 , THR A:270 , ILE A:273 , GOL A:316 , HOH A:373BINDING SITE FOR RESIDUE GOL A 315
2AC2SOFTWAREASN A:173 , TYR A:264 , GOL A:315 , GOL A:317 , HOH A:371 , GLY B:251BINDING SITE FOR RESIDUE GOL A 316
3AC3SOFTWAREMSE A:178 , PRO A:255 , MSE A:256 , LEU A:261 , GOL A:316 , HOH A:385 , ALA B:252 , HOH B:423BINDING SITE FOR RESIDUE GOL A 317
4AC4SOFTWAREPRO A:86 , LYS A:87 , GLU A:140 , ARG A:165 , LYS A:192 , HOH A:382BINDING SITE FOR RESIDUE GOL A 318
5AC5SOFTWAREASN B:220 , VAL B:224 , VAL B:265 , THR B:269 , THR B:270 , ILE B:273 , GOL B:317 , HOH B:368 , HOH B:531 , HOH B:552BINDING SITE FOR RESIDUE GOL B 315
6AC6SOFTWAREMSE B:38 , ALA B:119 , ILE B:120 , GLU B:122 , ASN B:147 , HOH B:332 , HOH B:354 , HOH B:449 , HOH B:524BINDING SITE FOR RESIDUE GOL B 316
7AC7SOFTWAREGLY A:251 , HOH A:394 , PHE B:172 , ASN B:173 , LEU B:223 , VAL B:265 , GOL B:315 , HOH B:356BINDING SITE FOR RESIDUE GOL B 317

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:173 -Pro A:174
2Asn B:173 -Pro B:174

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 10)

Asymmetric/Biological Unit (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024079A40THCDH_HUMANDisease (HADH deficiency)137853101A/BA40T
2UniProtVAR_024080D57EHCDH_HUMANDisease (HADH deficiency)137853102A/BD57E
3UniProtVAR_026764L86PHCDH_HUMANPolymorphism4956145A/BP86P
4UniProtVAR_055701Q152HHCDH_HUMANPolymorphism1051519A/BQ152H
5UniProtVAR_024081P258LHCDH_HUMANDisease (HHF4)137853103A/BP258L

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
13HCDHPS00067 3-hydroxyacyl-CoA dehydrogenase signature.HCDH_HUMAN213-237
 
  2A:213-237
B:213-237

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003095221cENSE00001196027chr4:108910940-108911220281HCDH_HUMAN1-44442A:23-44
B:1-44
22
44
1.4ENST000003095224ENSE00000333879chr4:108930915-108931043129HCDH_HUMAN45-87432A:45-87
B:45-87
43
43
1.5aENST000003095225aENSE00000841666chr4:108935587-108935744158HCDH_HUMAN88-140532A:88-140
B:88-140
53
53
1.6ENST000003095226ENSE00000841667chr4:108940696-108940822127HCDH_HUMAN140-182432A:140-182
B:140-182
43
43
1.7ENST000003095227ENSE00000841668chr4:108944630-10894471990HCDH_HUMAN183-212302A:183-212
B:183-212
30
30
1.8bENST000003095228bENSE00000841669chr4:108948844-10894891673HCDH_HUMAN213-237252A:213-237
B:213-237
25
25
1.10bENST0000030952210bENSE00000841670chr4:108954332-108954448117HCDH_HUMAN237-276402A:237-276
B:237-276
40
40
1.11dENST0000030952211dENSE00001561694chr4:108955395-108956331937HCDH_HUMAN276-314392A:276-314
B:276-314
39
39

(-) Sequences/Alignments

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:292
 aligned with HCDH_HUMAN | Q16836 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:292
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312  
           HCDH_HUMAN    23 KKIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENLKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains d3rqsa1 A:23-215 automated matches                                                                                                                                                               d3rqsa2 A:216-314 automated matches                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeee.hhhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhh...hhh.eeeee.........eeeeee....hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------T----------------E----------------------------P-----------------------------------------------------------------H---------------------------------------------------------------------------------------------------------L-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: A:213-237    ----------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1c  PDB: A:23-4Exon 1.4  PDB: A:45-87 UniProt: 45-87      Exon 1.5a  PDB: A:88-140 UniProt: 88-140             ------------------------------------------Exon 1.7  PDB: A:183-212      ------------------------Exon 1.10b  PDB: A:237-276              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: A:140-182 UniProt: 140-182  ------------------------------Exon 1.8b  PDB: A:213-237--------------------------------------Exon 1.11d  PDB: A:276-314              Transcript 1 (2)
                 3rqs A  23 KKIIVKHVTVIGGGLmGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVmKLVEVIKTPmTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLmEAIRLYERGDASKEDIDTAmKLGAGYPmGPFELLDYVGLDTTKFIVDGWHEmDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
                                    32     |  42        52        62        72        82        92       102       112       122       132       142       152       162       172     | 182     | 192       202       212       222     | 232       242     | 252   |   262       272       282       292       302       312  
                                          38-MSE                                                                                                                                     178-MSE   188-MSE                                 228-MSE             248-MSE 256-MSE                 280-MSE                              

Chain B from PDB  Type:PROTEIN  Length:316
 aligned with HCDH_HUMAN | Q16836 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:316
                              1                                                                                                                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308      
           HCDH_HUMAN     - --MAFVTRQFMRSVSSSSTASASAKKIIVKHVTVIGGGLMGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENLKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVMKLVEVIKTPMTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLMEAIRLYERGDASKEDIDTAMKLGAGYPMGPFELLDYVGLDTTKFIVDGWHEMDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------3HCDH_N-3rqsB03 B:29-214                                                                                                                                                                  -3HCDH-3rqsB01 B:216-313                                                                           - Pfam domains (1)
           Pfam domains (2) ------------------------------3HCDH_N-3rqsB04 B:29-214                                                                                                                                                                  -3HCDH-3rqsB02 B:216-313                                                                           - Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeee.hhhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhh...hhh.eeeee.........eeeeee....hhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhh....... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------T----------------E----------------------------P-----------------------------------------------------------------H---------------------------------------------------------------------------------------------------------L-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------3HCDH  PDB: B:213-237    ----------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) --Exon 1.1c  PDB: B:1-44 UniProt: 1-44        Exon 1.4  PDB: B:45-87 UniProt: 45-87      Exon 1.5a  PDB: B:88-140 UniProt: 88-140             ------------------------------------------Exon 1.7  PDB: B:183-212      ------------------------Exon 1.10b  PDB: B:237-276              -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------Exon 1.6  PDB: B:140-182 UniProt: 140-182  ------------------------------Exon 1.8b  PDB: B:213-237--------------------------------------Exon 1.11d  PDB: B:276-314              Transcript 1 (2)
                 3rqs B  -1 SHmAFVTRQFmRSVSSSSTASASAKKIIVKHVTVIGGGLmGAGIAQVAAATGHTVVLVDQTEDILAKSKKGIEESLRKVAKKKFAENPKAGDEFVEKTLSTIATSTDAASVVHSTDLVVEAIVENLKVKNELFKRLDKFAAEHTIFASNTSSLQITSIANATTRQDRFAGLHFFNPVPVmKLVEVIKTPmTSQKTFESLVDFSKALGKHPVSCKDTPGFIVNRLLVPYLmEAIRLYERGDASKEDIDTAmKLGAGYPmGPFELLDYVGLDTTKFIVDGWHEmDAENPLHQPSPSLNKLVAENKFGKKTGEGFYKYK 314
                              |      8|       18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278 |     288       298       308      
                              1-MSE   9-MSE                       38-MSE                                                                                                                                     178-MSE   188-MSE                                 228-MSE             248-MSE 256-MSE                 280-MSE                              

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RQS)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: 6PGD_C (47)
(-)
Family: 3HCDH (12)

(-) Gene Ontology  (17, 17)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        HCDH_HUMAN | Q168361f0y 1f12 1f14 1f17 1il0 1lsj 1lso 1m75 1m76 2hdh 3had

(-) Related Entries Specified in the PDB File

1f0y 100% HOMOLOGUE RELATED ID: HR487 RELATED DB: TARGETDB