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Title :   THE CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE SUBUNIT ALPHA FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC IN COMPLEX WITH ATP AND GLYCINE

Authors :   K. Tan, R. Zhang, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center Structural Genomics Of Infectious Diseases (Csgid)

Date :   08 Apr 11 (Deposition) - 08 Jun 11 (Release) - 08 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Alpha/Beta Protein, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Tan, R. Zhang, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Glycyl-Trna Synthetase Subunit Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc In Complex With Atp And Glycine.
To Be Published
PubMed: search

Molecule 1 - GLYCYL-TRNA SYNTHETASE ALPHA SUBUNIT
	Chains	:	A, B
	EC Number	:	6.1.1.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	CJ0704, GLYQ
	Organism Scientific	:	CAMPYLOBACTER JEJUNI
	Organism Taxid	:	197
	Strain	:	NCTC 11168
	Synonym	:	GLYCINE--TRNA LIGASE ALPHA SUBUNIT, GLYRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 20)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GLY	1	Mod. Amino Acid	GLYCINE
3	LMR	1	Ligand/Ion	(2S)-2-HYDROXYBUTANEDIOIC ACID
4	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:31 , GLY A:32 , THR A:33 , ARG A:58 , GLN A:76 , GLN A:78 , THR A:158 , ATP A:401	BINDING SITE FOR RESIDUE GLY A 301
2	AC2	SOFTWARE	ARG A:58 , ASP A:61 , ASN A:69 , ARG A:70 , LEU A:71 , TYR A:74 , GLN A:76 , MSE A:134 , GLU A:135 , VAL A:136 , THR A:137 , GLN A:138 , THR A:158 , GLY A:160 , GLY A:301	BINDING SITE FOR RESIDUE ATP A 401
3	AC3	SOFTWARE	ARG B:58 , ASP B:61 , ASN B:69 , LEU B:71 , TYR B:74 , GLU B:128 , GLU B:135 , VAL B:136 , THR B:137 , GLN B:138 , THR B:158 , GLY B:160 , ARG B:163	BINDING SITE FOR RESIDUE ATP B 401
4	AC4	SOFTWARE	SER B:117 , PRO B:118 , SER B:119 , MSE B:265	BINDING SITE FOR RESIDUE LMR B 501

(no "SS Bond" information available for 3RGL)

Asymmetric/Biological Unit

No.	Residues
1	Lys A:82	-	Pro A:83
2	Lys B:82	-	Pro B:83

(no "SAP(SNP)/Variant" information available for 3RGL)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_II_GLYAB	PS50861	Heterodimeric glycyl-transfer RNA synthetases family profile.	SYGA_CAMJE	2-280	2	A:2-280 B:2-280

(no "Exon" information available for 3RGL)

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:293
 aligned with SYGA_CAMJE | Q9PPK3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:294
                                    1                                                                                                                                                                                                                                                                                             
                                    |2        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    
           SYGA_CAMJE     - --------MTFSQMILNLQNYWQEQGCAIMQPYDMPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGMEVTQFTYFQQVGGIAVDLVSAEITYGLERIAMYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCMLAAHTFNLLDARGAISVAQRQDYMLKIRELSKNCAEIYKKNLNEA 286
               SCOP domains d3rgla_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.hhhhhhhhhhhhhhh...ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeee..eeehhhheeeeeeeeee...eeeeeeeeeee..ee.....eeeeeehhhhhhhhhh..hhhh.eeeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..-. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LIGASE_II_GLYAB  PDB: A:2-280 UniProt: 2-280                                                                                                                                                                                                                                   ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rgl A  -7 NLYFQSNAmTFSQmILNLQNYWQEQGCAImQPYDmPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGmEVTQFTYFQQVGGIAVDLVSAEITYGLERIAmYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCmLAAHTFNLLDARGAISVAQRQDYmLKIRELSKNCAEIYKKNLN-G 301
                                    |2   |    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 | |
                                    1-MSE|              22-MSE|                                                                                                        134-MSE                         166-MSE                                                                    241-MSE                 265-MSE            284 |
                                         6-MSE               27-MSE                                                                                                                                                                                                                                                            301

Chain B from PDB  Type:PROTEIN  Length:286
 aligned with SYGA_CAMJE | Q9PPK3 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:286
                              1                                                                                                                                                                                                                                                                                           
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      
           SYGA_CAMJE     - --MTFSQMILNLQNYWQEQGCAIMQPYDMPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGMEVTQFTYFQQVGGIAVDLVSAEITYGLERIAMYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCMLAAHTFNLLDARGAISVAQRQDYMLKIRELSKNCAEIYKKNLN 284
               SCOP domains d3rglb_ B: automated matches                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----tRNA-synt_2e-3rglB01 B:3-284                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ----tRNA-synt_2e-3rglB02 B:3-284                                                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhhhhhhh...ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhh..hhhhh.eeeee..eee....eeeeeeeeee...eeeeeeeeeee..ee.....eeeeeehhhhhhhhhh.......eeeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---AA_TRNA_LIGASE_II_GLYAB  PDB: B:2-280 UniProt: 2-280                                                                                                                                                                                                                                   ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rgl B  -1 NAmTFSQmILNLQNYWQEQGCAImQPYDmPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGmEVTQFTYFQQVGGIAVDLVSAEITYGLERIAmYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCmLAAHTFNLLDARGAISVAQRQDYmLKIRELSKNCAEIYKKNLN 284
                              |    | 8        18   |    28        38        48        58        68        78        88        98       108       118       128     | 138       148       158       168       178       188       198       208       218       228       238  |    248       258      |268       278      
                              |    |              22-MSE|                                                                                                        134-MSE                         166-MSE                                                                    241-MSE                 265-MSE               
                              1-MSE|                   27-MSE                                                                                                                                                                                                                                                             
                                   6-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Class II aaRS and biotin synthetases (165)

Superfamily: Class II aaRS and biotin synthetases (165)

Family: Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain (103)

Protein domain: automated matches (14)

Campylobacter jejuni [TaxId: 197] (2)

1a	d3rgla_	A:
1b	d3rglb_	B:

(no "CATH Domain" information available for 3RGL)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: tRNA_synt_II (64)

Family: tRNA-synt_2e (2)

Campylobacter jejuni (1)

1a	tRNA-synt_2e-3rglB01	B:3-284
1b	tRNA-synt_2e-3rglB02	B:3-284

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYGA_CAMJE | Q9PPK3)

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:0004820	glycine-tRNA ligase activity	Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0006426	glycyl-tRNA aminoacylation	The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'-adenosine residue of the tRNA.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
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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		Lys A:82 - Pro A:83	[ RasMol ]
		Lys B:82 - Pro B:83	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 3RGL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 20)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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