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Title :   CRYSTAL STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE-TRNA(PYL) COMPLEX FROM DESULFITOBACTERIUM HAFNIENSE

Authors :   K. Nozawa, Y. Araiso, D. Soll, R. Ishitani, O. Nureki

Date :   25 Apr 08 (Deposition) - 30 Dec 08 (Release) - 03 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Nozawa, P. O'Donoghue, S. Gundllapalli, Y. Araiso, R. Ishitani, T. Umehara, D. Soll, O. Nureki
Pyrrolysyl-Trna Synthetase-Trna(Pyl) Structure Reveals The Molecular Basis Of Orthogonality
Nature V. 457 1163 2009
PubMed-ID: 19118381 | Reference-DOI: 10.1038/NATURE07611
(for further references see the PDB file header)

Molecule 1 - PYRROLYSYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.26
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)CODONPLUS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PYLS
	Organism Scientific	:	DESULFITOBACTERIUM HAFNIENSE
	Organism Taxid	:	49338
	Synonym	:	BACTERIAL PROTEIN

Molecule 2 - BACTERIAL TRNA
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	TRANSCRIBED IN VITRO WITH T7 RNA POLYMERASE
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 13)

No.	Name	Count	Type	Full Name
1	CA	13	Ligand/Ion	CALCIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	G C:4	BINDING SITE FOR RESIDUE CA C 77
2	AC2	SOFTWARE	U C:65	BINDING SITE FOR RESIDUE CA C 78
3	AC3	SOFTWARE	G C:14	BINDING SITE FOR RESIDUE CA C 79
4	AC4	SOFTWARE	G C:9	BINDING SITE FOR RESIDUE CA C 81
5	AC5	SOFTWARE	G D:4	BINDING SITE FOR RESIDUE CA D 77
6	AC6	SOFTWARE	U D:65	BINDING SITE FOR RESIDUE CA D 78
7	AC7	SOFTWARE	G D:14	BINDING SITE FOR RESIDUE CA D 79
8	AC8	SOFTWARE	G D:9	BINDING SITE FOR RESIDUE CA D 81
9	AC9	SOFTWARE	U D:43	BINDING SITE FOR RESIDUE CA D 82

(no "SS Bond" information available for 2ZNI)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:148	-	Pro A:149
2	Gly A:236	-	Pro A:237
3	Lys B:148	-	Pro B:149
4	Gly B:236	-	Pro B:237

(no "SAP(SNP)/Variant" information available for 2ZNI)

(no "PROSITE Motif" information available for 2ZNI)

(no "Exon" information available for 2ZNI)

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:279
 aligned with B0S4P3_DESHA | B0S4P3 from UniProtKB/TrEMBL  Length:288

    Alignment length:279
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279         
         B0S4P3_DESHA    10 LSSFWTKVQYQRLKELNASGEQLEMGFSDALSRDRAFQGIEHQLMSQGKRHLEQLRTVKHRPALLELEEKLAKALHQQGFVQVVTPTIITKSALAKMTIGEDHPLFSQVFWLDGKKCLRPMLAPNLYTLWRELERLWDKPIRIFEIGTCYRKESQGAQHLNEFTMLNLTELGTPLEERHQRLEDMARWVLEAAGIREFELVTESSVVYGDTVDVMKGDLELASGAMGPHFLDEKWEIFDPWVGLGFGLERLLMIREGTQHVQSMARSLSYLDGVRLNIN 288
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------2zniA02 A:70-288 Bira Bifunctional Protein; Domain 2                                                                                                                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh..ee.....eeehhhhhh...................eee...hhhhhhhhhhhhhhhh...eeeeeeeeee...........eeeeeeeeee.....hhhhhhhhhhhhhhh.......eeee.........eeeee..eeeeeeeee...hhhhh.....eeeeeeehhhhhhhhh....................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zni A  10 LSSFWTKVQYQRLKELNASGEQLEMGFSDALSRDRAFQGIEHQLMSQGKRHLEQLRTVKHRPALLELEEKLAKALHQQGFVQVVTPTIITKSALAKMTIGEDHPLFSQVFWLDGKKCLRPMLAPNLYTLWRELERLWDKPIRIFEIGTCYRKESQGAQHLNEFTMLNLTELGTPLEERHQRLEDMARWVLEAAGIREFELVTESSVVYGDTVDVMKGDLELASGAMGPHFLDEKWEIFDPWVGLGFGLERLLMIREGTQHVQSMARSLSYLDGVRLNIN 288
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with B0S4P3_DESHA | B0S4P3 from UniProtKB/TrEMBL  Length:288

    Alignment length:279
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279         
         B0S4P3_DESHA    10 LSSFWTKVQYQRLKELNASGEQLEMGFSDALSRDRAFQGIEHQLMSQGKRHLEQLRTVKHRPALLELEEKLAKALHQQGFVQVVTPTIITKSALAKMTIGEDHPLFSQVFWLDGKKCLRPMLAPNLYTLWRELERLWDKPIRIFEIGTCYRKESQGAQHLNEFTMLNLTELGTPLEERHQRLEDMARWVLEAAGIREFELVTESSVVYGDTVDVMKGDLELASGAMGPHFLDEKWEIFDPWVGLGFGLERLLMIREGTQHVQSMARSLSYLDGVRLNIN 288
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------2zniB02 B:70-288 Bira Bifunctional Protein; Domain 2                                                                                                                                                                        CATH domains
           Pfam domains (1) ---------------------------------------------------------------tRNA-synt_2b-2zniB01 B:73-229                                                                                                                                ----------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------tRNA-synt_2b-2zniB02 B:73-229                                                                                                                                ----------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .....hhhhhhhhhhh..hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...ee.....eeehhhhhh...................eee...hhhhhhhhhhhhhh.....eeeeeeeeee...........eeeeeeeeee.....hhhhhhhhhhhhhhhhhh................eeeeee..eeeeeeeee.............eeeeee.hhhhhhhhh....hhhhh.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zni B  10 LSSFWTKVQYQRLKELNASGEQLEMGFSDALSRDRAFQGIEHQLMSQGKRHLEQLRTVKHRPALLELEEKLAKALHQQGFVQVVTPTIITKSALAKMTIGEDHPLFSQVFWLDGKKCLRPMLAPNLYTLWRELERLWDKPIRIFEIGTCYRKESQGAQHLNEFTMLNLTELGTPLEERHQRLEDMARWVLEAAGIREFELVTESSVVYGDTVDVMKGDLELASGAMGPHFLDEKWEIFDPWVGLGFGLERLLMIREGTQHVQSMARSLSYLDGVRLNIN 288
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279

Chain C from PDB  Type:RNA  Length:72
                                                                                                        
                 2zni C   1 GGGGGGUGGAUCGAAUAGAUCACACGGACUCUAAAUUCGUGCAGGCGGGUGAAACUCCCGUACUCCCCGCCA  76
                                  ||11   ||   23        33        43   ||   54        64        74  
                                  7|    15|                           47|                           
                                   9     18                            49

Chain D from PDB  Type:RNA  Length:72
                                                                                                        
                 2zni D   1 GGGGGGUGGAUCGAAUAGAUCACACGGACUCUAAAUUCGUGCAGGCGGGUGAAACUCCCGUACUCCCCGCCA  76
                                  ||11   ||   23        33        43   ||   54        64        74  
                                  7|    15|                           47|                           
                                   9     18                            49

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ 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 '\|'

(no "SCOP Domain" information available for 2ZNI)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: BirA Bifunctional Protein; domain 2 (111)

Homologous Superfamily: Bira Bifunctional Protein; Domain 2 (111)

Desulfitobacterium hafniense. Organism_taxid: 49338. (2)

1a	2zniA02	A:70-288
1b	2zniB02	B:70-288

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: tRNA_synt_II (64)

Family: tRNA-synt_2b (25)

Desulfitobacterium hafniense (Desulfitobacterium frappieri) (1)

1a	tRNA-synt_2b-2zniB01	B:73-229
1b	tRNA-synt_2b-2zniB02	B:73-229

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (B0S4P3_DESHA | B0S4P3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:236 - Pro A:237	[ RasMol ]
		Gly B:236 - Pro B:237	[ RasMol ]
		Lys A:148 - Pro A:149	[ RasMol ]
		Lys B:148 - Pro B:149	[ RasMol ]

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	2zni
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(no "Related Entries Specified in the PDB File" available for 2ZNI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 13)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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