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(-) Description

Title :  STRUCTURE OF AMINO ACID RACEMASE, 2.12 A
 
Authors :  H. Sakuraba, Y. Mutaguchi, J. Hayashi, T. Ohshima
Date :  12 Jan 17  (Deposition) - 19 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Plp-Dependent Enzyme, Fold Type I, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Hayashi, Y. Mutaguchi, Y. Minemura, N. Nakagawa, K. Yoneda, T. Ohmori, T. Ohshima, H. Sakuraba
Crystal Structure Of The Novel Amino-Acid Racemase Isoleucine 2-Epimerase From Lactobacillus Buchneri.
Acta Crystallogr D Struct V. 73 428 2017 Biol
PubMed-ID: 28471367  |  Reference-DOI: 10.1107/S2059798317005332

(-) Compounds

Molecule 1 - ISOLEUCINE 2-EPIMERASE
    Chains: A, B, C, D
    EC Number: 5.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD PROS2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: LACTOBACILLUS BUCHNERI
    Organism Taxid: 1581
    Synonym: BCAA RACEMASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 40)

Asymmetric/Biological Unit (2, 40)
No.NameCountTypeFull Name
1CD36Ligand/IonCADMIUM ION
2ILP4Ligand/IonN-[O-PHOSPHONO-PYRIDOXYL]-ISOLEUCINE

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:54 , SER A:114 , GLY A:115 , SER A:116 , TYR A:142 , HIS A:143 , GLU A:217 , ASP A:222 , ASP A:250 , VAL A:252 , ASN A:253 , LYS A:280 , ARG A:408 , HOH A:1117 , HOH A:1155 , HOH A:1167 , ALA B:83 , TYR B:84 , PHE B:308 , THR B:309 , HOH B:1119binding site for residue ILP A 1001
02AC2SOFTWAREASP A:5 , HIS A:241 , ASP A:274binding site for residue CD A 1002
03AC3SOFTWAREHIS A:33 , HOH A:1222binding site for residue CD A 1003
04AC4SOFTWAREHIS A:35 , HOH A:1221binding site for residue CD A 1004
05AC5SOFTWAREGLU A:64 , HOH A:1223binding site for residue CD A 1005
06AC6SOFTWAREHIS A:188 , GLU A:231binding site for residue CD A 1006
07AC7SOFTWAREHIS A:243 , HOH A:1216binding site for residue CD A 1007
08AC8SOFTWAREARG A:353 , HIS A:354 , GLU A:435 , HOH A:1218binding site for residue CD A 1008
09AC9SOFTWAREASP A:381binding site for residue CD A 1009
10AD1SOFTWAREHIS A:395binding site for residue CD A 1010
11AD2SOFTWAREGLU A:95 , GLU B:13binding site for residue CD A 1011
12AD3SOFTWAREALA A:83 , TYR A:84 , THR A:309 , ALA B:54 , SER B:114 , GLY B:115 , SER B:116 , TYR B:142 , HIS B:143 , GLU B:217 , ASP B:222 , ASP B:250 , ASN B:253 , LYS B:280 , ARG B:408 , HOH B:1122 , HOH B:1129 , HOH B:1143 , HOH B:1170binding site for residue ILP B 1001
13AD4SOFTWAREGLU A:13 , GLU B:95binding site for residue CD B 1002
14AD5SOFTWAREHIS B:33binding site for residue CD B 1003
15AD6SOFTWAREHIS B:35 , GLU B:64binding site for residue CD B 1004
16AD7SOFTWAREHIS B:188 , GLU B:231binding site for residue CD B 1005
17AD8SOFTWAREHIS B:243binding site for residue CD B 1006
18AD9SOFTWAREARG B:353 , HIS B:354 , GLU B:435binding site for residue CD B 1007
19AE1SOFTWAREASP B:381 , HOH B:1124 , HOH B:1206binding site for residue CD B 1008
20AE2SOFTWAREGLU B:418binding site for residue CD B 1009
21AE3SOFTWAREALA C:54 , SER C:114 , GLY C:115 , SER C:116 , TYR C:142 , HIS C:143 , GLU C:217 , ASP C:222 , ASP C:250 , VAL C:252 , ASN C:253 , LYS C:280 , ARG C:408 , HOH C:1133 , HOH C:1138 , HOH C:1147 , ALA D:83 , TYR D:84 , PHE D:308 , THR D:309 , HOH D:1110binding site for residue ILP C 1001
22AE4SOFTWAREHIS C:33 , HOH C:1194binding site for residue CD C 1002
23AE5SOFTWAREHIS C:35 , GLU C:64binding site for residue CD C 1003
24AE6SOFTWAREHIS C:188 , GLU C:231 , HOH C:1196binding site for residue CD C 1004
25AE7SOFTWAREASP C:5 , HIS C:241 , ASP C:274 , HOH C:1192binding site for residue CD C 1005
26AE8SOFTWAREHIS C:243binding site for residue CD C 1006
27AE9SOFTWAREARG C:353 , HIS C:354 , GLU C:435binding site for residue CD C 1007
28AF1SOFTWAREASP C:381binding site for residue CD C 1008
29AF2SOFTWAREHIS C:395binding site for residue CD C 1009
30AF3SOFTWAREGLU C:95 , HOH C:1124 , GLU D:13binding site for residue CD C 1010
31AF4SOFTWAREGLU C:328binding site for residue CD C 1011
32AF5SOFTWAREALA C:83 , TYR C:84 , PHE C:308 , THR C:309 , ALA D:54 , SER D:114 , GLY D:115 , SER D:116 , TYR D:142 , HIS D:143 , GLU D:217 , ASP D:222 , ASP D:250 , VAL D:252 , ASN D:253 , LYS D:280 , ARG D:408 , HOH D:1116 , HOH D:1118binding site for residue ILP D 1001
33AF6SOFTWAREHIS D:33binding site for residue CD D 1002
34AF7SOFTWAREHIS D:35 , GLU D:64binding site for residue CD D 1003
35AF8SOFTWAREHIS D:188 , GLU D:231 , HOH D:1177binding site for residue CD D 1004
36AF9SOFTWAREHIS D:243binding site for residue CD D 1005
37AG1SOFTWAREARG D:353 , HIS D:354 , GLU D:435binding site for residue CD D 1006
38AG2SOFTWAREASP D:381binding site for residue CD D 1007
39AG3SOFTWAREHIS D:395binding site for residue CD D 1008
40AG4SOFTWAREGLU C:13 , GLU D:95binding site for residue CD D 1009

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:164 -Pro A:165
2Ala A:303 -Pro A:304
3Gly B:164 -Pro B:165
4Ala B:303 -Pro B:304
5Gly C:164 -Pro C:165
6Ala C:303 -Pro C:304
7Gly D:164 -Pro D:165
8Ala D:303 -Pro D:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WYF)

(-) 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:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wyf A   1 MGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTIGKIGW 450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  441|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   446    


Chain B from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wyf B   3 KLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTIGKIGW 450
                                    12        22        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       322       332       342       352       362       372       382       392       402       412       422       432       446    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                441|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 446    


Chain C from PDB  Type:PROTEIN  Length:446
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wyf C   1 MGKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTIGKIGW 450
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  441|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   446    


Chain D from PDB  Type:PROTEIN  Length:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh........eehhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhh...hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5wyf D   3 KLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTIGKIGW 450
                                    12        22        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       322       332       342       352       362       372       382       392       402       412       422       432       446    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                441|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 446
   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 5WYF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Ala D:303 - Pro D:304   [ RasMol ]  
    Gly A:164 - Pro A:165   [ RasMol ]  
    Gly B:164 - Pro B:165   [ RasMol ]  
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  5wyf
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  5.1.1.21
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 Related Entries

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

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        ILE2E_LACBU | M1GRN3: 4ysn 4ysv 5ll2 5ll3 5wya

(-) Related Entries Specified in the PDB File

5wya