3RF1 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF GLYCYL-TRNA SYNTHETASE SUBUNIT ALPHA FROM CAMPYLOBACTER JEJUNI SUBSP. JEJUNI NCTC 11168

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

Date :   05 Apr 11 (Deposition) - 20 Apr 11 (Release) - 20 Apr 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Glycyl-Trna Synthetase Subunit Alpha, 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, J. Hasseman, W. F. Anderson, A. Joachimiak
The Crystal Structure Of Glycyl-Trna Synthetase Subunit Alpha From Campylobacter Jejuni Subsp. Jejuni Nctc 11168
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	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLYQ, CJJ81176_0727
	Organism Scientific	:	CAMPYLOBACTER JEJUNI
	Organism Taxid	:	354242
	Strain	:	81-176
	Synonym	:	GLYCINE-TRNA LIGASE ALPHA SUBUNIT, GLYRS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 23)

No.	Name	Count	Type	Full Name
1	GOL	5	Ligand/Ion	GLYCEROL
2	LMR	2	Ligand/Ion	(2S)-2-HYDROXYBUTANEDIOIC ACID
3	MSE	16	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:58 , ASN A:69 , ARG A:70 , LEU A:71	BINDING SITE FOR RESIDUE LMR A 288
2	AC2	SOFTWARE	ARG A:57 , PHE A:200 , TYR A:203 , ASN A:204 , HIS A:245 , LEU A:249 , HOH A:291	BINDING SITE FOR RESIDUE GOL A 289
3	AC3	SOFTWARE	ARG B:163	BINDING SITE FOR RESIDUE LMR B 288
4	AC4	SOFTWARE	GLY B:44 , LYS B:45 , LYS B:46 , LYS B:280 , LEU B:283 , ASN B:284	BINDING SITE FOR RESIDUE GOL B 289
5	AC5	SOFTWARE	PRO A:24 , ASP A:26 , PRO B:24 , TYR B:25 , MSE B:27 , HIS B:35 , ALA B:54 , PRO B:55 , HOH B:295	BINDING SITE FOR RESIDUE GOL B 290
6	AC6	SOFTWARE	GLN A:216 , ASN A:219 , GLN B:216 , ASN B:219 , SER B:220	BINDING SITE FOR RESIDUE GOL B 291
7	AC7	SOFTWARE	SER B:117 , HOH B:303	BINDING SITE FOR RESIDUE GOL B 292

(no "SS Bond" information available for 3RF1)

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 3RF1)

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_CAMJJ	2-280	2	A:2-280 B:2-280

(no "Exon" information available for 3RF1)

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:292
 aligned with SYGA_CAMJJ | A1VZ59 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:292
                                    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_CAMJJ     - --------MTFSQMILNLQNYWQEQGCAIMQPYDMPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGMEVTQFTYFQQVGGIAVDLVSAEITYGLERIAMYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCMLAAHTFNLLDARGAISVAQRQDYMLKIRELSKNCAEIYKKNLN 284
               SCOP domains d3rf1a_ 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..eee....eeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhh...hhhh.eeeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------AA_TRNA_LIGASE_II_GLYAB  PDB: A:2-280 UniProt: 2-280                                                                                                                                                                                                                                   ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rf1 A  -7 NLYFQSNAmTFSQmILNLQNYWQEQGCAImQPYDmPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGmEVTQFTYFQQVGGIAVDLVSAEITYGLERIAmYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCmLAAHTFNLLDARGAISVAQRQDYmLKIRELSKNCAEIYKKNLN 284
                                    |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               
                                         6-MSE               27-MSE

Chain B from PDB  Type:PROTEIN  Length:285
 aligned with SYGA_CAMJJ | A1VZ59 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:285
                             1                                                                                                                                                                                                                                                                                           
                             |       9        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     
           SYGA_CAMJJ     - -MTFSQMILNLQNYWQEQGCAIMQPYDMPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGMEVTQFTYFQQVGGIAVDLVSAEITYGLERIAMYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCMLAAHTFNLLDARGAISVAQRQDYMLKIRELSKNCAEIYKKNLN 284
               SCOP domains d3rf1b_ B: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---tRNA-synt_2e-3rf1B01 B:3-284                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ---tRNA-synt_2e-3rf1B02 B:3-284                                                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh..ee.........hhhhhhhhhh.......eeeeeeeeee.hhhh..........eeeeeeeeee....hhhhhhhhhhhhhh.......eeeee..eee....eeeeeeeeee..eeeeeeeeeeee..ee.....eeeeeehhhhhhhhhh.......eeeee..eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --AA_TRNA_LIGASE_II_GLYAB  PDB: B:2-280 UniProt: 2-280                                                                                                                                                                                                                                   ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rf1 B   0 AmTFSQmILNLQNYWQEQGCAImQPYDmPAGAGTFHPATFLRSLGKKPWAAAYVAPSRRPTDGRYGENPNRLGAYYQFQVLIKPSPDNIQELYLKSLENLGFDLKSHDIRFVEDNWESPSLGAWGLGWEVWLDGmEVTQFTYFQQVGGIAVDLVSAEITYGLERIAmYLQNVDNVYDIVWSEFNGEKIKYADVHKQSEYEFSKYNFEVSDVKILNEQFENSYKECKNILEQGLALPAYDYCmLAAHTFNLLDARGAISVAQRQDYmLKIRELSKNCAEIYKKNLN 284
                             |    |  9        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     
                             1-MSE|              22-MSE|                                                                                                        134-MSE                         166-MSE                                                                    241-MSE                 265-MSE               
                                  6-MSE               27-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: 354242] (1)

1a	d3rf1a_	A:
1b	d3rf1b_	B:

(no "CATH Domain" information available for 3RF1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: tRNA_synt_II (64)

Family: tRNA-synt_2e (2)

Campylobacter jejuni subsp. jejuni serotype O:23/36 (strain 81-176) (1)

1a	tRNA-synt_2e-3rf1B01	B:3-284
1b	tRNA-synt_2e-3rf1B02	B:3-284

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SYGA_CAMJJ | A1VZ59)

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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		LMR	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Lys A:82 - Pro A:83	[ RasMol ]
		Lys B:82 - Pro B:83	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3rf1
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SYGA_CAMJJ \| A1VZ59
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	6.1.1.14
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SYGA_CAMJJ \| A1VZ59
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 3RF1)

(no "Related Entries Specified in the PDB File" available for 3RF1)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 23)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File