2ZIO - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH ALOCLYS-AMP AND PNP

Authors :   T. Yanagisawa, R. Ishii, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   19 Feb 08 (Deposition) - 02 Dec 08 (Release) - 09 Dec 08 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.06

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

Keywords :   Aminoacyl-Trna Synthetase, Pyrrolysyl-Trna Synthetase, Trna, Pyrrolysine, Atp Analogue, Non-Natural Amino Acid, Unnatural Amino Acid, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Yanagisawa, R. Ishii, R. Fukunaga, T. Kobayashi, K. Sakamoto, S. Yokoyama
Multistep Engineering Of Pyrrolysyl-Trna Synthetase To Genetically Encode N(Varepsilon)-(O-Azidobenzyloxycarbonyl) Lysine For Site-Specific Protein Modification
Chem. Biol. V. 15 1187 2008
PubMed-ID: 19022179 | Reference-DOI: 10.1016/J.CHEMBIOL.2008.10.004
(for further references see the PDB file header)

Compounds

Molecule 1 - PYRROLYSYL-TRNA SYNTHETASE
	Chains	:	A
	EC Number	:	6.1.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28C
	Expression System Strain	:	BL21(DE3) CODON PLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL FRAGMENT
	Gene	:	PYLS
	Organism Scientific	:	METHANOSARCINA MAZEI
	Organism Taxid	:	2209
	Strain	:	JCM9314
	Synonym	:	PYRROLYSINE--TRNA LIGASE, PYLRS

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	2PN	1	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	AYB	1	Ligand/Ion	5'-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	2PN	2	Ligand/Ion	IMIDODIPHOSPHORIC ACID
2	AYB	2	Ligand/Ion	5'-O-[(S)-({(2S)-2-AMINO-6-[(PROPOXYCARBONYL)AMINO]HEXANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:338 , LEU A:395 , GLU A:396 , ARG A:426 , HOH A:753	BINDING SITE FOR RESIDUE 2PN A 1
2	AC2	SOFTWARE	ALA A:302 , LEU A:309 , ARG A:330 , GLU A:332 , GLU A:337 , LEU A:339 , PHE A:342 , MET A:344 , ASN A:346 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , TRP A:417 , ALA A:420 , GLY A:421 , GLY A:423 , ARG A:426 , HOH A:604 , HOH A:608 , HOH A:637 , HOH A:640 , HOH A:684 , HOH A:705 , HOH A:753	BINDING SITE FOR RESIDUE AYB A 601

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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)
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	UniProt sequence: complete aligned part

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Chain A from PDB  Type:PROTEIN  Length:255
 aligned with PYLS_METMA | Q8PWY1 from UniProtKB/Swiss-Prot  Length:454

    Alignment length:267
                                   197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       
           PYLS_METMA   188 PALTKSQTDRLEVLLNPKDEISLNSGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDNDTELSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDGKEHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGDSCMVYGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSESYYNGISTNL 454
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2zioA01 A:188-239 He    lix hairpin bin             2zioA02 A:240-454 Bira Bifunctional Prote   in; Domain 2                                                                                                                                                                CATH domains
               Pfam domains --------------------    ------------------------------tRNA-synt_2b-2zioA01 A:242-379                                                                                                                ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.....----...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eee....eeehhhhhh.....---......ee...eee...hhhhhhhhhhhhh......eeeeeeeeee......-....eeeeeeeeee....hhhhhhhhhhhhhhhhh...eee..----...eeeeee..eeeeeeee..hhhhhhhh....eeeeeeehhhhhhhhhh..hhhhh.....ee..ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zio A 188 PALTKSQTDRLEVLLNPKDE----SGKPFRELESELLSRRKKDLQQIYAEERENYLGKLEREITRFFVDRGFLEIKSPILIPLEYIERMGIDN---LSKQIFRVDKNFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRKESDG-EHLEEFTMLNFCQMGSGCTRENLESIITDFLNHLGIDFKIVGD----YGDTLDVMHGDLELSSAVVGPIPLDREWGIDKPWIGAGFGLERLLKVKHDFKNIKRAARSGSYYNGISTNL 454
                                   197       207    |  217       227       237       247       257       267       277  |   |287       297       307       317       327       337       347       357       367       377 |    |387       397       407       417       427       437       447       
                                             207  212                                                                 280 284                                                335 |                                       379  384                                                                      
                                                                                                                                                                               337

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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)

CATH Domains (2, 2)

Pfam Domains (1, 1)

Gene Ontology (10, 10)

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