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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A S-SELECTIVE TRANSAMINASE FROM BACILLUS MEGATERIUM BOUND WITH R-ALPHA-METHYLBENZYLAMINE
 
Authors :  N. Van Oosterwijk, S. Willies, J. Hekelaar, A. C. Terwisscha Van Sch N. J. Turner, B. W. Dijkstra
Date :  17 Mar 16  (Deposition) - 27 Jul 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transferase, Transaminase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Van Oosterwijk, S. Willies, J. Hekelaar, A. C. Terwisscha Van Scheltinga, N. J. Turner, B. W. Dijkstra
Structural Basis Of Substrate Range And Enantioselectivity Of Two S-Selective Omega- Transaminases
Biochemistry V. 55 4422 2016
PubMed-ID: 27428867  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00370

(-) Compounds

Molecule 1 - TRANSAMINASE
    Chains: A, B, C, D
    EC Number: 2.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA II
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Other Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND TO R- ALPHA-METHYLBENZYLAMINE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
26DF4Ligand/Ion[6-METHYL-5-OXIDANYL-4-[(~{E})-[(1~{R})-1-PHENYLETHYL]IMINOMETHYL]PYRIDIN-3-YL]METHYLDIHYDROGEN PHOSPHATE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5PGE8Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:121 , SER A:122 , TYR A:148 , HIS A:149 , GLY A:150 , GLU A:237 , ASP A:269 , VAL A:271 , LEU A:272 , LYS A:298 , HOH A:2097 , HOH A:2116 , HOH A:2186 , HOH A:2214 , HOH A:2290 , SER B:329 , THR B:330BINDING SITE FOR RESIDUE 6DF A1475
02AC2SOFTWARETYR A:135 , ARG A:138 , GLY A:263 , LEU A:265 , GLU A:315 , HOH A:2106 , HOH A:2198BINDING SITE FOR RESIDUE PGE A1476
03AC3SOFTWAREASN A:137 , HOH A:2291 , HOH A:2292 , ASN C:137BINDING SITE FOR RESIDUE PGE A1477
04AC4SOFTWAREGLU A:428 , LYS A:429 , ASP A:459 , TYR A:463BINDING SITE FOR RESIDUE 1PE A1478
05AC5SOFTWAREPHE A:56 , TYR A:164 , VAL A:436 , HOH A:2037 , HOH A:2293 , HOH A:2294 , TRP B:86 , THR B:88BINDING SITE FOR RESIDUE PGE A1479
06AC6SOFTWARETHR A:330 , HOH A:2098 , HOH A:2233 , HOH A:2234 , HOH A:2236 , LEU B:59 , GLY B:121 , SER B:122 , TYR B:148 , HIS B:149 , GLY B:150 , GLU B:237 , ALA B:242 , ASP B:269 , VAL B:271 , LYS B:298 , HOH B:2143BINDING SITE FOR RESIDUE 6DF B1474
07AC7SOFTWARETYR B:135 , THR B:136 , GLY B:263 , GLU B:315 , HOH B:2090BINDING SITE FOR RESIDUE PGE B1475
08AC8SOFTWARETRP A:86 , TYR A:89 , HOH A:2064 , PHE B:56 , VAL B:436 , HOH B:2111BINDING SITE FOR RESIDUE PGE B1476
09AC9SOFTWAREGLY C:121 , SER C:122 , TYR C:148 , HIS C:149 , GLY C:150 , GLU C:237 , ASP C:269 , VAL C:271 , LYS C:298 , HOH C:2094 , HOH C:2095 , HOH C:2116 , HOH C:2160 , HOH C:2237 , THR D:330BINDING SITE FOR RESIDUE 6DF C1475
10BC1SOFTWAREARG C:138 , GLY C:263 , LEU C:265 , GLU C:315 , HOH C:2104BINDING SITE FOR RESIDUE PGE C1476
11BC2SOFTWARETRP C:86 , THR C:88 , TYR C:89 , HOH C:2060 , HOH C:2238 , PHE D:56 , VAL D:436BINDING SITE FOR RESIDUE PGE C1477
12BC3SOFTWAREGLU C:428 , LYS C:429 , TYR C:463BINDING SITE FOR RESIDUE PGE C1480
13BC4SOFTWAREPHE C:56 , TYR C:164 , VAL C:436 , HOH C:2039 , TRP D:86 , THR D:88 , TYR D:89 , HOH D:2175 , HOH D:2176BINDING SITE FOR RESIDUE PG4 D1475
14BC5SOFTWARESER C:329 , THR C:330 , HOH C:2096 , HOH C:2207 , HOH C:2208 , HOH C:2210 , GLY D:121 , SER D:122 , TYR D:148 , HIS D:149 , GLU D:237 , ALA D:242 , ASP D:269 , VAL D:271 , LYS D:298 , HOH D:2104BINDING SITE FOR RESIDUE 6DF D1476
15BC6SOFTWARETHR D:136 , GLY D:263 , HOH D:2061BINDING SITE FOR RESIDUE PEG D1477
16BC7SOFTWARESER A:177 , ASN B:137 , ASN D:137BINDING SITE FOR RESIDUE PG4 D1480

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G09)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:82 -Gly A:83
2Tyr B:82 -Gly B:83
3Tyr C:82 -Gly C:83
4Tyr D:82 -Gly D:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5G09)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G09)

(-) Exons   (0, 0)

(no "Exon" information available for 5G09)

(-) 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:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh................eee..eee.....eeee.hhhhhh......hhhhhhhhhhhh...........hhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh..hhhhh..ee.......ee..........eeee....................hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhh......eeeeeehhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhh...ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g09 A   7 KINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQA 475
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466         


Chain B from PDB  Type:PROTEIN  Length:471
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh................eee..eee.....eeee.hhhhhh......hhhhhhhhhhhh...........hhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh..hhhhh..ee.......ee..........eeee....................hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhh......eeeeeehhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g09 B   3 LTVQKINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEW 473
                                    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       442       452       462       472 


Chain C from PDB  Type:PROTEIN  Length:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh................eee..eee.....eeee.hhhhhh......hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh..hhhhh..ee...................eeee....................hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhh......eeeeeehhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g09 C   7 KINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQA 475
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466         


Chain D from PDB  Type:PROTEIN  Length:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh................eee..eee.....eeee.hhhhhh......hhhhhhhhhhhh...........hhhhhhhhhhhhh........eeeeeee.hhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh..hhhhh..ee...................eeee....................hhhhhhhhhhhhhhh...eeeeee.............hhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhh......eeeeeehhhhhhhhh.ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g09 D   2 SLTVQKINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQ 474
                                    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       451       461       471
   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 5G09)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G09)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G09)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5G09)

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    Tyr A:82 - Gly A:83   [ RasMol ]  
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    Tyr D:82 - Gly D:83   [ RasMol ]  
 

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5g0a THE CRYSTAL STRUCTURE OF A S-SELECTIVE TRANSAMINASE FROM BACILLUS MEGATERIUM