2YKU - JenaLib

Title :   STRUCTURAL DETERMINANTS OF THE BETA-SELECTIVITY OF A BACTERIAL AMINOTRANSFERASE

Authors :   G. G. Wybenga, C. G. Crismaru, D. B. Janssen, B. W. Dijkstra

Date :   30 May 11 (Deposition) - 30 May 12 (Release) - 29 Aug 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: C  (2x)
Biol. Unit 2: A,B  (1x)

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. G. Wybenga, C. G. Crismaru, D. B. Janssen, B. W. Dijkstra
Structural Determinants Of The Beta-Selectivity Of A Bacterial Aminotransferase.
J. Biol. Chem. V. 287 28495 2012
PubMed-ID: 22745123 | Reference-DOI: 10.1074/JBC.M112.375238

Compounds

Molecule 1 - BETA-TRANSAMINASE
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MESORHIZOBIUM SP. LUK
	Organism Taxid	:	398267
	Other Details	:	SCHIFF BASE BETWEEN K280 ETA-AMINE AND THE C4A OF THE PLP COFACTOR
	Synonym	:	BETA-PHENYLALANINE AMINOTRANSFERASE

Structural Features

Chains, Units

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (2x)	:			C
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 18)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	EDO	13	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	PLP	3	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 10)

No.	Name	Count	Type	Full Name
1	EDO	8	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	-1	Ligand/Ion	GLYCEROL
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
2	GOL	2	Ligand/Ion	GLYCEROL
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Sites (19, 19)

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:144 , GLY A:145 , THR A:146 , ASN A:149 , TYR A:172 , HIS A:173 , GLU A:220 , ASP A:253 , VAL A:255 , MET A:256 , LYS A:280 , HOH A:2230 , HOH A:2286 , HOH A:2441 , THR B:314	BINDING SITE FOR RESIDUE PLP A1280
02	AC2	SOFTWARE	LEU A:124 , GLU A:127 , ALA A:128 , HIS A:326 , THR A:330 , HOH A:2201 , HOH A:2347 , ARG C:43 , GLU C:120 , HOH C:2032	BINDING SITE FOR RESIDUE GOL A1446
03	AC3	SOFTWARE	LEU A:124 , GLU A:127 , ALA A:128 , HIS A:326 , THR A:330 , HOH A:2201 , HOH A:2347 , ARG C:43 , GLU C:120 , HOH C:2032	BINDING SITE FOR RESIDUE GOL A1446
04	AC4	SOFTWARE	ARG A:240 , SER A:244 , ARG B:305 , ASP B:306	BINDING SITE FOR RESIDUE EDO A1447
05	AC5	SOFTWARE	ARG A:335 , GLN A:336 , SER A:339 , ASP C:33 , HIS C:80	BINDING SITE FOR RESIDUE EDO A1448
06	AC6	SOFTWARE	ALA A:20 , ILE A:23 , ALA A:24 , ARG A:27 , THR A:160 , ARG A:162 , HOH A:2237	BINDING SITE FOR RESIDUE GOL A1449
07	AC7	SOFTWARE	THR A:314 , HOH A:2224 , HOH A:2225 , HOH A:2342 , SER B:144 , GLY B:145 , THR B:146 , ASN B:149 , TYR B:172 , HIS B:173 , GLU B:220 , ASP B:253 , VAL B:255 , MET B:256 , LYS B:280 , EDO B:1449 , HOH B:2179 , HOH B:2237	BINDING SITE FOR RESIDUE PLP B1280
08	AC8	SOFTWARE	ALA B:225 , GLY B:226 , GLY B:227 , THR B:373 , LYS B:395 , ARG B:412 , HOH B:2239 , HOH B:2240 , HOH B:2363	BINDING SITE FOR RESIDUE EDO B1445
09	AC9	SOFTWARE	ASN B:198 , ASP B:199 , ARG B:382 , HOH B:2225 , HOH B:2227	BINDING SITE FOR RESIDUE EDO B1446
10	BC1	SOFTWARE	SER B:72 , VAL B:83 , GLU B:420 , ALA B:422 , GLY B:425	BINDING SITE FOR RESIDUE EDO B1447
11	BC2	SOFTWARE	GLU B:232 , ALA B:234 , HOH B:2245 , PRO C:380	BINDING SITE FOR RESIDUE EDO B1448
12	BC3	SOFTWARE	SER C:144 , GLY C:145 , THR C:146 , ASN C:149 , TYR C:172 , HIS C:173 , GLY C:174 , GLU C:220 , ASP C:253 , VAL C:255 , MET C:256 , LYS C:280 , THR C:314 , HOH C:2166 , HOH C:2169 , HOH C:2191 , HOH C:2227	BINDING SITE FOR RESIDUE PLP C1280
13	BC4	SOFTWARE	HIS C:80 , ALA C:81 , TYR C:82 , LEU C:403 , ARG C:404	BINDING SITE FOR RESIDUE EDO C1448
14	BC5	SOFTWARE	GLU A:120 , HOH A:2181 , ARG B:43 , LEU C:124 , GLU C:127 , ALA C:128 , HIS C:326 , HOH C:2147 , HOH C:2284	BINDING SITE FOR RESIDUE EDO C1449
15	BC6	SOFTWARE	HIS C:40 , ALA C:44 , GLU C:120 , ALA C:123 , HOH C:2032 , HOH C:2127 , HOH C:2138	BINDING SITE FOR RESIDUE EDO C1450
16	BC7	SOFTWARE	ASP B:33 , HIS B:80 , HOH B:2025 , ARG C:335 , GLN C:336 , SER C:339	BINDING SITE FOR RESIDUE EDO C1451
17	BC8	SOFTWARE	ILE A:56 , TYR A:172 , ALA A:180 , ARG A:412 , HOH A:2443	BINDING SITE FOR RESIDUE EDO A1450
18	BC9	SOFTWARE	HOH A:2342 , HOH A:2344 , ILE B:56 , TYR B:172 , LYS B:280 , PLP B:1280	BINDING SITE FOR RESIDUE EDO B1449
19	CC1	SOFTWARE	ALA B:81 , TYR B:82 , LEU B:403 , ARG B:404 , GLY B:406 , HOH B:2026	BINDING SITE FOR RESIDUE EDO B1450

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:433
 aligned with A3EYF7_9RHIZ | A3EYF7 from UniProtKB/TrEMBL  Length:445

    Alignment length:433
                                    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   
         A3EYF7_9RHIZ    13 ASDTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALLM 445
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.....................eeeeee..hhhhhhhhhhhhh..eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee..hhhhhh.hhhhhhhh....eeeee.hhhh....eeeeehhhhhhhhh...............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.ee.....eee.....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yku A  13 ASDTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALLM 445
                                    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

Chain B from PDB  Type:PROTEIN  Length:430
 aligned with A3EYF7_9RHIZ | A3EYF7 from UniProtKB/TrEMBL  Length:445

    Alignment length:430
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444
         A3EYF7_9RHIZ    15 DTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALL 444
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.....................eeeeee..hhhhhhhhhhhhh..eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee..hhhhhh.hhhhhhhh....eeeee.hhhh....eeeeehhhhhhhhh...............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.ee.....eee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yku B  15 DTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALL 444
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444

Chain C from PDB  Type:PROTEIN  Length:432
 aligned with A3EYF7_9RHIZ | A3EYF7 from UniProtKB/TrEMBL  Length:445

    Alignment length:432
                                    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  
         A3EYF7_9RHIZ    13 ASDTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALL 444
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.hhhhh.......eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhhhhhh..eeeeee.....................eeeeee..hhhhhhhhhhhhh..eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee..hhhhh..hhhhhhhh....eeeee.hhhh....eeeeehhhhhhhhh...............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.ee.....eee.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yku C  13 ASDTAEKAQAIAAARNTFARDNPVSAGHHERARRSMPGGNTRSILFHRPFPLVIAQGTGSRFQDVDGHAYVNFLGEYTAGLFGHSHPVIRAAVERALAVGLNLSTQTENEALFAEAVCDRFPSIDLVRFTNSGTEANLMALATATAITGRKTVLAFDGGYHGGLLNFASGHAPTNAPYHVVLGVYNDVEGTADLLKRHGHDCAAILVEPMLGAGGCVPAERAFLDLLRAEASRCGALLIFDEVMTSRLSGGGAQEMLGISADLTTLGKYIGGGMSFGAFGGRRDLMERFDPARDGAFAHAGTFNNNILTMSAGHAALTQIYTRQAASDLSASGDRFRANLNRIAVENQAPLQFTGLGSLGTIHFSRAPIRSAGDVRAADQQLKELFFFHMLRKGIYLAPRGMYALSLEIADAGRDAFAEALADFIGEQRALL 444
                                    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

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Classification and Annotation

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

2ykv	STRUCTURAL DETERMINANTS OF THE BETA-SELECTIVITY OF A BACTERIAL AMINOTRANSFERASE
2ykx	STRUCTURAL DETERMINANTS OF THE BETA-SELECTIVITY OF A BACTERIAL AMINOTRANSFERASE
2yky	STRUCTURAL DETERMINANTS OF THE BETA-SELECTIVITY OF A BACTERIAL AMINOTRANSFERASE
4ao4	STRUCTURAL DETERMINANTS OF THE BETA-SELECTIVITY OF A BACTERIAL AMINOTRANSFERASE

Description