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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE 1 (RPMFE1) COMPLEXED WITH 3S-HYDROXY-DECANOYL-COA, 3-KETO-DECANOYL-COA AND NADH
 
Authors :  P. Kasaragod, W. Schmitz, J. Kalervo Hiltunen, R. K. Wierenga
Date :  26 Jul 15  (Deposition) - 08 Jun 16  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, 3S-Hydroxy-Decanoyl-Coa, 3-Keto-Decanoyl-Coa, Nadh, Mfe1, Beta-Oxidation, Fatty Acid, Crotonase, 3-Hydroxyacyl-Coa- Dehydrogenase, Hydratase, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kasaragod, W. Schmitz, J. Kalervo Hiltunen, R. K. Wierenga
Crystal Strucuture Of Mfe1 Ternanry Complex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEROXISOMAL BIFUNCTIONAL ENZYME
    Chains: A, B
    EC Number: 4.2.1.17, 5.3.3.8, 1.1.1.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET15B
    Expression System Vector Type: PLASMID
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: 3S-HYDROXY-DECANOYL-COA BOUND IN THE CROTONASE DOMAIN AND, 3-KETO-DECANOYL-COA AND NADH BOUND IN THE 3-HYDROXYACYL-COA-DEHYDROGENASE DOMAIN.
    Synonym: PBE, PBFE, MULTIFUNCTIONAL ENZYME TYPE-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 11)

Asymmetric Unit (6, 11)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HSC2Ligand/Ion(S)-3-HYDROXYDECANOYL-COA
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PO41Ligand/IonPHOSPHATE ION
5SO44Ligand/IonSULFATE ION
6ZOZ1Ligand/Ion3-KETO-DECANOYL-COA
Biological Unit 1 (5, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HSC1Ligand/Ion(S)-3-HYDROXYDECANOYL-COA
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PO4-1Ligand/IonPHOSPHATE ION
5SO42Ligand/IonSULFATE ION
6ZOZ1Ligand/Ion3-KETO-DECANOYL-COA
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HSC1Ligand/Ion(S)-3-HYDROXYDECANOYL-COA
3NAD-1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4PO41Ligand/IonPHOSPHATE ION
5SO42Ligand/IonSULFATE ION
6ZOZ-1Ligand/Ion3-KETO-DECANOYL-COA

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:30 , LYS A:677 , LYS A:680BINDING SITE FOR RESIDUE GOL A1721
02AC2SOFTWAREARG A:641BINDING SITE FOR RESIDUE SO4 A1722
03AC3SOFTWARELEU A:302 , GLY A:305 , THR A:306 , MET A:307 , GLU A:326 , SER A:327 , GLN A:331 , ALA A:380 , VAL A:381 , GLU A:383 , LYS A:388 , ASN A:408 , SER A:410 , ALA A:524 , ZOZ A:1726 , HOH A:2142BINDING SITE FOR RESIDUE NAD A1723
04AC4SOFTWAREPRO A:191 , ILE A:192 , GLU A:193 , ARG A:196 , HOH A:2085 , HOH A:2239 , HOH A:2240BINDING SITE FOR RESIDUE SO4 A1724
05AC5SOFTWAREPRO A:20 , VAL A:21 , ALA A:23 , VAL A:24 , PRO A:26 , ILE A:29 , ALA A:59 , GLY A:60 , ALA A:61 , ASP A:62 , ILE A:63 , PHE A:66 , LEU A:98 , GLY A:100 , GLU A:103 , GLU A:123 , LEU A:126 , PRO A:130 , GLY A:131 , TYR A:156 , LYS A:275 , HOH A:2241 , HOH A:2242BINDING SITE FOR RESIDUE HSC A1725
06AC6SOFTWARETHR A:342 , ARG A:349 , SER A:410 , HIS A:431 , SER A:434 , HIS A:437 , VAL A:438 , MET A:439 , ASN A:481 , LYS A:514 , MET A:515 , TYR A:653 , NAD A:1723 , HOH A:2143 , HOH A:2243BINDING SITE FOR RESIDUE ZOZ A1726
07AC7SOFTWAREPHE B:492 , SER B:521 , LEU B:526 , GLY B:529 , ARG B:533 , HOH B:2095BINDING SITE FOR RESIDUE PO4 B1718
08AC8SOFTWAREGLN A:94 , ASN A:114 , SER A:174 , ASP A:175 , SER B:67 , PHE B:69 , THR B:70BINDING SITE FOR RESIDUE GOL B1719
09AC9SOFTWAREILE B:192 , GLU B:193 , ARG B:196BINDING SITE FOR RESIDUE SO4 B1720
10BC1SOFTWAREGLY B:305 , THR B:306 , HOH B:2082 , HOH B:2133BINDING SITE FOR RESIDUE SO4 B1721
11BC2SOFTWAREPRO B:20 , VAL B:21 , ALA B:59 , ALA B:61 , ASP B:62 , ILE B:63 , PHE B:66 , LEU B:73 , LEU B:98 , GLY B:100 , GLU B:103 , PRO B:122 , GLU B:123 , LEU B:126 , PRO B:130 , GLY B:131 , ALA B:132 , TYR B:156 , PHE B:255 , LYS B:275 , LYS B:279 , HOH B:2077 , HOH B:2134 , HOH B:2135BINDING SITE FOR RESIDUE HSC B1722

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AAJ)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Pro A:19 -Pro A:20
2Thr A:70 -Pro A:71
3Ser A:434 -Pro A:435
4Pro B:19 -Pro B:20
5Ser B:434 -Pro B:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AAJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AAJ)

(-) Exons   (0, 0)

(no "Exon" information available for 5AAJ)

(-) Sequences/Alignments

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:726
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee...eeeeee........hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh......hhhhhhhhhhhh....eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhh....eee..hhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh...........ee.hhhhhh...eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhh.......eeeee.........eeeeee....hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..............ee..ee..hhhhhhhhh....hhhh...eee.......eeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5aaj A  -5 VPRGSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGSPPLKEWQSLAGPHGS 720
                                     4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714      


Chain B from PDB  Type:PROTEIN  Length:718
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee........hhhhhhhhhhhhhhhhh.....eeeeee.........hhhhh.......hhhhhhhhhhh....eeeee..eeehhhhhhhhhh.eeeee...eeehhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eehhhhhh.....eee..hhhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhh......eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhh.............eeee.hhhhh....eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhh..hhh.eeeeee........eeeeee....hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..............ee..ee..hhhhhhhhh....hhhh....ee.......ee.hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5aaj B   0 HMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGSPPLKEWQSLAGP 717
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709
   Legend:   → Mismatch (orange background)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AAJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AAJ)

(-) Gene Ontology  (18, 18)

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        ECHP_RAT | P07896: 1zcj 2x58 3zw8 3zw9 3zwa 3zwb 3zwc 5mgb

(-) Related Entries Specified in the PDB File

5aak CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NAD