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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST D3,D2-ENOYL-COA ISOMERASE F268A MUTANT
 
Authors :  G. U. Onwukwe, M. K. Koski, R. K. Wierenga
Date :  17 Apr 15  (Deposition) - 11 Nov 15  (Release) - 18 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Crotonase, Isomerase, Beta-Oxidation, Enoyl-Coa Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. U. Onwukwe, M. K. Koski, P. Pihko, W. Schmitz, R. K. Wierenga
Structures Of Yeast Peroxisomal Delta (3), Delta (2)-Enoyl-Coa Isomerase Complexed With Acyl-Coa Substrate Analogues: The Importance Of Hydrogen-Bond Networks For The Reactivity Of The Catalytic Base And The Oxyanion Hole.
Acta Crystallogr. , Sect. D V. 71 2178 2015
PubMed-ID: 26527136  |  Reference-DOI: 10.1107/S139900471501559X

(-) Compounds

Molecule 1 - 3,2-TRANS-ENOYL-COA ISOMERASE
    Chains: A, B, C
    EC Number: 5.3.3.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ECI1, YLR284C
    Mutation: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: DELTA(3),DELTA(2)-ENOYL-COA ISOMERASE,D3,D2-ENOYL-COA ISOMERASE,DODECENOYL-COA ISOMERASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO414Ligand/IonSULFATE ION
Biological Unit 1 (2, 34)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2SO428Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:70 , PHE A:97 , ARG A:100 , GLY A:125 , LEU A:126 , LEU A:155 , GLU A:158 , HOH A:403binding site for residue GOL A 301
02AC2SOFTWAREARG A:64 , PRO A:202 , SER A:203 , SER A:204binding site for residue SO4 A 302
03AC3SOFTWARESER A:62 , GLY A:63 , ALA A:206 , GLU A:207 , HOH A:419 , HOH A:467binding site for residue SO4 A 303
04AC4SOFTWARETYR A:225 , PRO A:227 , HOH A:452 , LYS B:257 , ASP B:261binding site for residue SO4 A 304
05AC5SOFTWARELYS A:257 , TYR A:258 , TYR C:225binding site for residue SO4 A 305
06AC6SOFTWAREGLU A:9 , ILE A:25 , ASN A:26binding site for residue SO4 A 306
07AC7SOFTWAREALA B:70 , PHE B:97 , ARG B:100 , GLY B:125 , LEU B:126 , PHE B:150 , LEU B:155 , GLU B:158 , HOH B:456binding site for residue GOL B 301
08AC8SOFTWAREARG B:64 , LYS B:143 , PRO B:202 , SER B:203 , SER B:204binding site for residue SO4 B 302
09AC9SOFTWARESER B:62 , GLY B:63 , ALA B:206 , GLU B:207 , SO4 B:304 , HOH B:405 , HOH B:411binding site for residue SO4 B 303
10AD1SOFTWARESO4 B:303 , HOH B:422 , HOH B:446binding site for residue SO4 B 304
11AD2SOFTWAREGLU B:9 , ILE B:25 , ASN B:26binding site for residue SO4 B 305
12AD3SOFTWAREGLY C:69 , ALA C:70 , ARG C:100 , GLY C:125 , LEU C:126 , LEU C:155 , GLU C:158 , HOH C:425binding site for residue GOL C 301
13AD4SOFTWAREARG C:64 , LYS C:143 , PRO C:202 , SER C:203 , SER C:204binding site for residue SO4 C 302
14AD5SOFTWAREGLY C:63 , SER C:204 , ALA C:206 , GLU C:207binding site for residue SO4 C 303
15AD6SOFTWARESER C:12 , HIS C:23 , ILE C:25binding site for residue SO4 C 304
16AD7SOFTWARETYR B:225 , PRO B:227 , LYS C:257 , TYR C:258 , ASP C:261binding site for residue SO4 C 305
17AD8SOFTWAREGLU C:9 , ASN C:26binding site for residue SO4 C 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZDE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZDE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZDE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZDE)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDE)

(-) 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:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhhhh.eeee.....eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhh....ee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zde A   3 QEIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRARQL 271
                                    12        22        32        42        52        62        72 ||     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262         
                                                                                                  74|                                                                                                                                                                                          
                                                                                                   85                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhhhh.eeee.....eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhh....ee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zde B   4 EIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRARQ 270
                                    13        23        33        43        53        63        73||      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
                                                                                                 74|                                                                                                                                                                                         
                                                                                                  85                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhhhhh....eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee...eehhhhhhhhhh.eeee.....eee.hhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhh..eeee......hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zde C   4 EIRQNEKISYRIEGPFFIIHLINPDNLNALEGEDYIYLGELLELADRNRDVYFTIIQSSGRFFSSGADFKGKYPSETSKWVSNFVARNVYVTDAFIKHSKVLICCLNGPAIGLSAALVALCDIVYSINDKVYLLYPFANLGLITEGGTTVSLPLKFGTNTTYECLMFNKPFKYDIMCENGFISKNFNMPSSNAEAFNAKVLEELREKVKGLYLPSCLGMKKLLKSNHIDAFNKANSVEVNESLKYWVDGEPLKRAR 269
                                    13        23        33        43        53        63        73||      93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      
                                                                                                 74|                                                                                                                                                                                        
                                                                                                  85
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  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 4ZDE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZDE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZDE)

(-) Gene Ontology  (8, 8)

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