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(-) Description

Title :  STRUCTURE OF AMINO ACID RACEMASE, 2.65 A
 
Authors :  H. Sakuraba, Y. Mutaguchi, J. Hayashi, T. Ohshima
Date :  11 Jan 17  (Deposition) - 19 Apr 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Fold Type I, Plp-Dependent Enzyme, 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, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
17VO4Ligand/Ion(2S,3S)-3-METHYL-2-[[2-METHYL-3-OXIDANYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLAMINO]PENTANOICACID
2DMS11Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:24 , ALA A:54 , SER A:114 , GLY A:115 , SER A:116 , TYR A:142 , HIS A:143 , GLU A:217 , ASP A:250 , VAL A:252 , ASN A:253 , LYS A:280 , ARG A:408 , HOH A:1107 , HOH A:1117 , TYR B:84 , LEU B:307 , PHE B:308 , THR B:309 , HOH B:1124binding site for residue 7VO A 1001
02AC2SOFTWARESER A:178 , GLU A:187 , LYS A:227 , PRO A:229 , TRP A:363 , HOH A:1205binding site for residue DMS A 1002
03AC3SOFTWAREGLN A:133 , LYS D:162 , GLY D:164binding site for residue DMS A 1003
04AC4SOFTWARELYS A:162 , GLY A:164 , HOH A:1207 , ARG B:127 , GLY B:131 , GLU D:210binding site for residue DMS A 1004
05AC5SOFTWARETYR A:182 , GLU A:185binding site for residue DMS A 1005
06AC6SOFTWARETYR A:84 , LEU A:307 , PHE A:308 , THR A:309 , HOH A:1132 , ALA B:54 , SER B:114 , GLY B:115 , SER B:116 , TYR B:142 , HIS B:143 , GLU B:217 , ASP B:250 , VAL B:252 , ASN B:253 , LYS B:280 , ARG B:408 , HOH B:1140 , HOH B:1156binding site for residue 7VO B 1001
07AC7SOFTWARESER B:178 , LYS B:227 , TRP B:363 , HOH B:1181binding site for residue DMS B 1002
08AC8SOFTWAREPHE B:202 , GLU B:203binding site for residue DMS B 1003
09AC9SOFTWAREGLN B:133 , LYS C:162 , GLY C:164 , HOH C:2224 , ARG D:127 , ARG D:132binding site for residue DMS B 1004
10AD1SOFTWARETYR B:182 , HOH B:1104 , GLU C:185 , HOH C:2165binding site for residue DMS C 2001
11AD2SOFTWAREALA C:54 , SER C:114 , GLY C:115 , SER C:116 , TYR C:142 , HIS C:143 , GLU C:217 , ASP C:250 , VAL C:252 , ASN C:253 , LYS C:280 , ARG C:408 , HOH C:2111 , HOH C:2119 , TYR D:84 , PHE D:308 , THR D:309 , HOH D:1127binding site for residue 7VO C 2002
12AD3SOFTWARESER C:178binding site for residue DMS C 2003
13AD4SOFTWAREPHE C:202 , HIS C:243binding site for residue DMS C 2004
14AD5SOFTWARETYR C:84 , LEU C:307 , 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:1108 , HOH D:1112 , HOH D:1156binding site for residue 7VO D 1001
15AD6SOFTWARELYS D:46binding site for residue DMS D 1002

(-) SS Bonds  (0, 0)

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

(-) 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 5WYA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5WYA)

(-) 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:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh......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
                 5wya A   3 KLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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         


Chain B from PDB  Type:PROTEIN  Length:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh......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..ee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wya B   2 GKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441


Chain C from PDB  Type:PROTEIN  Length:440
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh......eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhh..hhhhh.........eeee............hhhhhhhhhhhhhhhhhhh..hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee..ee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wya C   2 GKLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441


Chain D from PDB  Type:PROTEIN  Length:439
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               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............hhhhhhhhhhhhhhhhhhh..hhh.eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh......eeeehhhhhh....eeeeeehhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee.........hhhhhhhhhhhhhhh.ee..ee...eeee......hhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5wya D   3 KLDKASKLIDEENKYYARSARINYYNLVIDHAHGATLVDVDGNKYIDLLASASAINVGHTHEKVVKAIADQAQKLIHYTPAYFHHVPGMELSEKLAKIAPGNSPKMVSFGNSGSDANDAIIKFARAYTGRQYIVSYMGSYHGSTYGSQTLSGSSLNMTRKIGPMLPSVVHVPYPDSYRTYPGETEHDVSLRYFNEFKKPFESFLPADETACVLIEPIQGDGGIIKAPEEYMQLVYKFCHEHGILFAIDEVNQGLGRTGKMWAIQQFKDIEPDLMSVGKSLASGMPLSAVIGKKEVMQSLDAPAHLFTTAGNPVCSAASLATLDVIEYEGLVEKSATDGAYAKQRFLEMQQRHPMIGDVRMWGLNGGIELVKDPKTKEPDSDAATKVIYYAFAHGVVIITLAGNILRFQPPLVIPREQLDQALQVLDDAFTAVENGEVTI 441
                                    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
   Legend:   → Mismatch (orange background)
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    → 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 5WYA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  ILE2E_LACBU | M1GRN3
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 Related Entries

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

(-) Related Entries Specified in the PDB File

5wyf