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(-) Description

Title :  THE CRYSTAL STRUCTURE OF A S-SELECTIVE TRANSAMINASE FROM BACILLUS MEGATERIUM
 
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 :  1.70
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 Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA II
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Other Details: PYRIDOXAL-5'-PHOSPHATE COVALENTLY BOUND TO LYSINE 298

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
3PG45Ligand/IonTETRAETHYLENE GLYCOL
4PGE3Ligand/IonTRIETHYLENE GLYCOL
5PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:56 , LEU A:59 , TYR A:148 , TYR A:164 , LYS A:298 , VAL A:436 , PLP A:1298 , HOH A:2063 , THR B:88 , TYR B:89BINDING SITE FOR RESIDUE 1PE A1475
02AC2SOFTWAREGLU A:428 , LYS A:429 , ASP A:459 , TYR A:463BINDING SITE FOR RESIDUE 1PE A1476
03AC3SOFTWAREARG A:256 , LYS A:260 , GLN A:290 , PRO A:291 , ASP A:292 , HOH A:2268BINDING SITE FOR RESIDUE PEG A1477
04AC4SOFTWAREPHE A:176 , SER A:177 , HOH A:2194 , ASN B:137 , ALA C:178 , ASN D:137BINDING SITE FOR RESIDUE 1PE A1478
05AC5SOFTWARETYR A:135 , GLY A:263 , GLU A:315 , HOH A:2146 , HOH A:2252 , HOH A:2371BINDING SITE FOR RESIDUE PGE A1479
06AC6SOFTWAREPHE A:25 , SER A:26 , HOH A:2026 , HOH A:2335 , ARG B:324 , HOH B:2231BINDING SITE FOR RESIDUE PEG B1475
07AC7SOFTWARETYR B:135 , ARG B:138 , GLY B:263 , LEU B:265 , GLU B:315 , HOH B:2106 , HOH B:2234BINDING SITE FOR RESIDUE PGE B1476
08AC8SOFTWAREARG B:256 , LYS B:260 , GLN B:290 , PRO B:291 , ASP B:292 , GLU B:315 , HOH B:2235BINDING SITE FOR RESIDUE PEG B1477
09AC9SOFTWARETHR A:88 , TYR A:89 , HOH A:2093 , VAL B:34 , PHE B:56 , LEU B:59 , VAL B:436 , HOH B:2020BINDING SITE FOR RESIDUE PG4 B1478
10BC1SOFTWAREARG C:256 , LYS C:260 , GLN C:290 , PRO C:291 , ASP C:292 , GLU C:315 , PG4 C:1478 , HOH C:2039 , HOH C:2209BINDING SITE FOR RESIDUE PEG C1475
11BC2SOFTWAREASN A:137 , SER B:177 , ASN C:137BINDING SITE FOR RESIDUE PG4 C1476
12BC3SOFTWAREPHE C:56 , LEU C:59 , VAL C:436 , HOH C:2057 , THR D:88 , TYR D:89BINDING SITE FOR RESIDUE PG4 C1477
13BC4SOFTWARETYR C:135 , ARG C:138 , GLY C:263 , GLU C:315 , PEG C:1475 , HOH C:2133 , HOH C:2208BINDING SITE FOR RESIDUE PG4 C1478
14BC5SOFTWARELYS C:429 , ASP C:459 , TYR C:463BINDING SITE FOR RESIDUE PG4 C1479
15BC6SOFTWARETHR C:88 , TYR C:89 , HOH C:2085 , PHE D:56 , LEU D:59 , TYR D:164 , LEU D:272 , VAL D:436BINDING SITE FOR RESIDUE 1PE D1475
16BC7SOFTWARETYR D:135 , GLY D:263 , LEU D:265 , GLU D:315 , HOH D:2081 , HOH D:2138 , HOH D:2204BINDING SITE FOR RESIDUE PGE D1476
17BC8SOFTWARELEU A:59 , CYS A:61 , GLY A:121 , SER A:122 , TYR A:148 , HIS A:149 , GLU A:237 , ASP A:269 , VAL A:271 , LEU A:272 , GLY A:297 , GLY A:299 , LEU A:300 , SER A:301 , SER A:302 , SER A:303 , 1PE A:1475 , HOH A:2136 , HOH A:2160 , HOH A:2240 , HOH A:2272 , HOH A:2369 , THR B:330 , TYR B:331BINDING SITE FOR DI-PEPTIDE LYS A 298 AND PLP A1298
18BC9SOFTWARETHR A:330 , TYR A:331 , HOH A:2137 , HOH A:2290 , HOH A:2291 , LEU B:59 , CYS B:61 , GLY B:121 , SER B:122 , TYR B:148 , HIS B:149 , GLU B:237 , ASP B:269 , VAL B:271 , LEU B:272 , GLY B:297 , GLY B:299 , LEU B:300 , SER B:301 , SER B:302 , SER B:303 , HOH B:2160 , HOH B:2188BINDING SITE FOR DI-PEPTIDE LYS B 298 AND PLP B1298
19CC1SOFTWARELEU C:59 , CYS C:61 , GLY C:121 , SER C:122 , TYR C:148 , HIS C:149 , GLY C:150 , GLU C:237 , ASP C:269 , VAL C:271 , LEU C:272 , GLY C:297 , GLY C:299 , LEU C:300 , SER C:301 , SER C:302 , SER C:303 , HOH C:2123 , HOH C:2149 , HOH C:2197 , HOH C:2226 , HOH C:2228 , HOH C:2285 , THR D:330 , TYR D:331BINDING SITE FOR DI-PEPTIDE LYS C 298 AND PLP C1298
20CC2SOFTWARETHR C:330 , TYR C:331 , HOH C:2124 , HOH C:2247 , HOH C:2248 , HOH C:2250 , LEU D:59 , CYS D:61 , GLY D:121 , SER D:122 , TYR D:148 , HIS D:149 , GLU D:237 , ASP D:269 , VAL D:271 , LEU D:272 , GLY D:297 , GLY D:299 , LEU D:300 , SER D:301 , SER D:302 , SER D:303 , HOH D:2128 , HOH D:2153BINDING SITE FOR DI-PEPTIDE LYS D 298 AND PLP D1298

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5G0A)

(-) 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 5G0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5G0A)

(-) Exons   (0, 0)

(no "Exon" information available for 5G0A)

(-) 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:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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
                 5g0a A   7 KINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQ 474
                                    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:473
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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......hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g0a B   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   


Chain C from PDB  Type:PROTEIN  Length:468
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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......eeeeeehhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5g0a C   7 KINWEQVKEWDRKYLMRTFSTQNEYQPVPIESTEGDYLIMPDGTRLLDFFNQLYCVNLGQKNQKVNAAIKEALDRYGFVWDTYATDYKAKAAKIIIEDILGDEDWPGKVRFVSTGSEAVETALNIARLYTNRPLVVTREHDYHGWTGGAATVTRLRSYRSGLVGENSESFSAQIPGSSYNSAVLMAPSPNMFQDSDGNLLKDENGELLSVKYTRRMIENYGPEQVAAVITEVSQGAGSAMPPYEYIPQIRKMTKELGVLWINDEVLTGFGRTGKWFGYQHYGVQPDIITMGKGLSSSSLPAGAVLVSKEIAAFMDKHRWESVSTYAGHPVAMAAVCANLEVMMEENFVEQAKDSGEYIRSKLELLQEKHKSIGNFDGYGLLWIVDIVNAKTKTPYVKLDRNFTHGMNPNQIPTQIIMKKALEKGVLIGGVMPNTMRIGASLNVSRGDIDKAMDALDYALDYLESGEWQ 474
                                    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............hhhhhh.....eeeehhhhh......eeeeeehhhhhhhh..ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee...........hhhhh....hhhhhhhhhhhhhhhh..ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5g0a 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
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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 5G0A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5G0A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5G0A)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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    Tyr D:82 - Gly D:83   [ RasMol ]  
 

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5g09 THE CRYSTAL STRUCTURE OF A S-SELECTIVE TRANSAMINASE FROM BACILLUS MEGATERIUM BOUND WITH R-ALPHA- METHYLBENZYLAMINE