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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT PEROXISOMAL MULTIFUNCTIONAL ENZYME 2 TYPE-1 (RPMFE1) COMPLEXED WITH ACETOACETYL-COA AND NAD
 
Authors :  P. Kasaragod, T. -R. Kiema, W. Schmitz, J. K. Hiltunen, R. K. Wierenga
Date :  21 Nov 16  (Deposition) - 21 Dec 16  (Release) - 08 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Acetoacetyl-Coa, Nad+, Mfe1, Beta-Oxidation, Fatty Acid, Crotonase, 3-Hydroxyacyl-Coa-Dehydrogenase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kasaragod, G. Balcha, S. Sridhar, W. Schmitz, T. -R. Kiema, J. K. 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 BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EHHADH
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PBFE

 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  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1CAA2Ligand/IonACETOACETYL-COENZYME A
2GOL2Ligand/IonGLYCEROL
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1CAA1Ligand/IonACETOACETYL-COENZYME A
2GOL2Ligand/IonGLYCEROL
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CAA1Ligand/IonACETOACETYL-COENZYME A
2GOL-1Ligand/IonGLYCEROL
3NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
4SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:191 , ILE A:192 , GLU A:193 , ARG A:196binding site for residue SO4 A 801
02AC2SOFTWAREGLY A:262 , HOH A:938binding site for residue SO4 A 802
03AC3SOFTWAREARG A:641binding site for residue SO4 A 803
04AC4SOFTWAREPRO A:20 , VAL A:21 , ALA A:59 , GLY A:60 , ALA A:61 , ASP A:62 , ILE A:63 , PHE A:66 , GLY A:100 , GLU A:103 , ARG A:118 , GLU A:123 , TYR A:156 , LYS B:249binding site for residue CAA A 804
05AC5SOFTWARELEU A:302 , GLY A:303 , GLY A:305 , THR A:306 , MET A:307 , GLU A:326 , SER A:327 , GLN A:331 , ALA A:380 , VAL A:381 , PHE A:382 , GLU A:383 , LYS A:388 , VAL A:391 , ASN A:408 , SER A:410 , HIS A:431 , PHE A:432 , SER A:434binding site for residue NAD A 805
06AC6SOFTWARELYS A:265 , PHE A:664 , ALA A:667 , SER A:668 , PRO A:707 , LEU A:708 , HOH A:924binding site for residue GOL A 806
07AC7SOFTWAREPRO A:548 , ARG A:550 , HIS A:606binding site for residue GOL A 807
08AC8SOFTWAREPRO B:191 , ILE B:192 , GLU B:193binding site for residue SO4 B 801
09AC9SOFTWAREPRO B:20 , VAL B:21 , ALA B:59 , GLY B:60 , ALA B:61 , ASP B:62 , ILE B:63 , PHE B:66 , LEU B:75 , GLY B:100 , GLU B:103 , PRO B:122 , GLU B:123 , GLY B:131 , TYR B:156 , LYS B:275 , LYS B:463binding site for residue CAA B 802
10AD1SOFTWARETHR A:597 , LEU B:302 , GLY B:303 , GLY B:305 , THR B:306 , MET B:307 , GLU B:326 , SER B:327 , GLN B:331 , VAL B:381 , PHE B:382 , GLU B:383 , LYS B:388 , VAL B:391 , ASN B:408 , SER B:410 , HIS B:431 , PHE B:432 , SER B:434 , HOH B:905binding site for residue NAD B 803

(-) SS Bonds  (0, 0)

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

(-) 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 5MGB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MGB)

(-) 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:725
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeeeee........hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh......hhhhhhhhhhhh....eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhh....eee..hhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.hhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhh..hhh.eeeee.........eeeeee....hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..............ee..ee..hhhhhhhhh...hhhhh...eee.......eeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mgb A  -4 PRGSHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGSPPLKEWQSLAGPHGS 720
                                     5        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       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715     


Chain B from PDB  Type:PROTEIN  Length:720
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee....eeeeee........hhhhhhhhhhhhhhhhhh....eeeeee.........hhhhh.......hhhhhhhhhhh....eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.eeehhhhhhh....eee..hhhhhhhhhhhh.....hhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................eeeee..hhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhh...........eeee.hhhhhhhh.eeee....hhhhhhhhhhhhhhhh....eeee.....hhhhhhhh..hhh.eeeee.........eeeeee....hhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..............ee..ee..hhhhhhhhh...hhhhh...eee.......eeehhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mgb B  -1 SHMAEYLRLPHSLAMIRLCNPPVNAVSPTVIREVRNGLQKAGSDHTVKAIVICGANGNFCAGADIHGFSAFTPGLALGSLVDEIQRYQKPVLAAIQGVALGGGLELALGCHYRIANAKARVGLPEVTLGILPGARGTQLLPRVVGVPVALDLITSGKYLSADEALRLGILDAVVKSDPVEEAIKFAQKIIDKPIEPRRIFNKPVPSLPNMDSVFAEAIAKVRKQYPGVLAPETCVRSIQASVKHPYEVGIKEEEKLFMYLRASGQAKALQYAFFAEKSANKWSTPSGASWKTASAQPVSSVGVLGLGTMGRGIAISFARVGISVVAVESDPKQLDAAKKIITFTLEKEASRAHQNGQASAKPKLRFSSSTKELSTVDLVVEAVFEDMNLKKKVFAELSALCKPGAFLCTNTSALNVDDIASSTDRPQLVIGTHFFSPAHVMRLLEVIPSRYSSPTTIATVMSLSKKIGKIGVVVGNCYGFVGNRMLAPYYNQGFFLLEEGSKPEDVDGVLEEFGFKMGPFRVSDLAGLDVGWKIRKGQGLTGPSLPPGTPVRKRGNSRYSPLGDMLCEAGRFGQKTGKGWYQYDKPLGRIHKPDPWLSTFLSQYREVHHIEQRTISKEEILERCLYSLINEAFRILEEGMAARPEHIDVIYLHGYGWPRHKGGPMFYAASVGLPTVLEKLQKYYRQNPDIPQLEPSDYLRRLVAQGSPPLKEWQSLAGPH 718
                                     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       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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

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