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(-) Description

Title :  CRYSTAL STRUCTURE OF PROLYL-TRNA SYNTHETASE FROM METHANOTHERMOBACTER THERMAUTOTROPHICUS BOUND TO CYSTEINE SULFAMOYL ADENYLATE
 
Authors :  S. Kamtekar, W. D. Kennedy, J. Wang, C. Stathopoulos, D. Soll, T. A. Stei
Date :  30 Dec 02  (Deposition) - 04 Mar 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Protein-Aminoacyladenylate Complex Class-Ii Trna Synthetase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Kamtekar, W. D. Kennedy, J. Wang, C. Stathopoulos, D. Soll, T. A. Steitz
The Structural Basis Of Cysteine Aminoacylation Of Trnapro By Prolyl-Trna Synthetases
Proc. Natl. Acad. Sci. Usa V. 100 1673 2003
PubMed-ID: 12578991  |  Reference-DOI: 10.1073/PNAS.0437911100

(-) Compounds

Molecule 1 - PROLINE-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21DE3 RECA-
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N TERMINALLY HIS TAGGED ENZYME
    Gene: MTH611
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262
    Other Details: STRAIN SUPPLEMENTED WITH ADDITIONAL PLASMID ENCODING RARE TRNAS
    Synonym: PROLYL-TRNA SYNTHETASE;
PROLINE--TRNA LIGASE;
PRORS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
15CA1Ligand/Ion5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE
2MG1Ligand/IonMAGNESIUM ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15CA2Ligand/Ion5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE
2MG-1Ligand/IonMAGNESIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:436 , CYS A:441 , CYS A:464 , CYS A:467BINDING SITE FOR RESIDUE ZN A 513
2AC2SOFTWAREASP A:210 , GLU A:446 , ASP A:452 , HOH A:492 , HOH A:493BINDING SITE FOR RESIDUE MG A 514
3AC3SOFTWARETHR A:117 , GLU A:119 , ARG A:148 , GLU A:150 , ILE A:158 , ARG A:159 , VAL A:160 , ILE A:163 , PHE A:166 , GLU A:168 , PHE A:212 , GLN A:232 , GLY A:234 , THR A:235 , HIS A:237 , GLY A:267 , SER A:269 , ARG A:271 , HOH A:487BINDING SITE FOR RESIDUE 5CA A 512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NJ1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:136 -Pro A:137

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 1NJ1)

(-) 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:463
 aligned with SYP_METTH | O26708 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:463
                                    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       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478   
            SYP_METTH    19 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRILDRDHEEVLFPLLVPEDELAKEAIHVKGFEDEVYWVTHGGLSKLQRKLALRPTSETVMYPMFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLITRRPPWDKFPGSEYTVAFDTLMPDGKTLQIGTVHNLGQTFARTFEIKFETPEGDHEYVHQTCYGLSDRVIASVIAIHGDESGLCLPPDVAAHQVVIVPIIFKKAAEEVMEACRELRSRLEAAGFRVHLDDRDIRAGRKYYEWEMRGVPLRVEIGPRDLEKGAAVISRRDTGEKVTADLQGIEETLRELMKDILENLRTRAWERMESEIREAETLEEASRIVDEKRGIISFMWCGEEECGMDVEEKVRVDILGIQEEGSGTCINCGREAPTGLTLPEHI 481
               SCOP domains d1nj1a3 A:19-283 Prolyl-tRNA synthetase (ProRS)                                                                                                                                                                                                                          d1nj1a1 A:284-410 Prolyl-tRNA synthetase (ProRS) domain                                                                        d1nj1a2 A:411-481 C-terminal domain of ProRS                            SCOP domains
               CATH domains 1nj1A01 A:19-289 Bira Bifunctional Protein; Domain 2                                                                                                                                                                                                                           1nj1A02 A:290-393  [code=3.40.50.800, no name defined]                                                  -----------------1nj1A03 A:411-480  [code=3.30.110.30, no name defined]                - CATH domains
               Pfam domains ----------------------------------tRNA-synt_2b-1nj1A03 A:53-226                                                                                                                                                 ---------------------------------------------------------------------HGTP_anticodon-1nj1A01 A:296-391                                                                -------------------------ProRS-C_1-1nj1A02 A:417-472                             --------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..ee.........eehhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhh.hhhhhhhh.....eeeee..eeeeeeeee...hhhhhhhhhhhhh.......eeeeeeeeee..............eeeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh....eeee...........eeeeeeee.....eeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeee.hhhhhhhhhhh.....ee.........eeeee.....hhhhhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhee..eeeeehhhhhh..eeeeee.....eeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eee..hhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhh.eeeeeee..............eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nj1 A  19 EFSEWFHNILEEAEIIDQRYPVKGMHVWMPHGFMIRKNTLKILRRILDRDHEEVLFPLLVPEDELAKEAIHVKGFEDEVYWVTHGGLSKLQRKLALRPTSETVMYPMFALWVRSHTDLPMRFYQVVNTFRYETKHTRPLIRVREITTFKEAHTIHATASEAEEQVERAVEIYKEFFNSLGIPYLITRRPPWDKFPGSEYTVAFDTLMPDGKTLQIGTVHNLGQTFARTFEIKFETPEGDHEYVHQTCYGLSDRVIASVIAIHGDESGLCLPPDVAAHQVVIVPIIFKKAAEEVMEACRELRSRLEAAGFRVHLDDRDIRAGRKYYEWEMRGVPLRVEIGPRDLEKGAAVISRRDTGEKVTADLQGIEETLRELMKDILENLRTRAWERMESEIREAETLEEASRIVDEKRGIISFMWCGEEECGMDVEEKVRVDILGIQEEGSGTCINCGREAPYRAYLARTY 481
                                    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       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: IIaaRS-ABD (13)
(-)
Clan: no clan defined [family: ProRS-C_1] (4)
(-)
Clan: tRNA_synt_II (64)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYP_METTH | O26708)
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: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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0004827    proline-tRNA ligase activity    Catalysis of the reaction: ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006433    prolyl-tRNA aminoacylation    The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-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: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.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SYP_METTH | O26708: 1nj2 1nj5 1nj6

(-) Related Entries Specified in the PDB File

1nj2 1nj5 1nj6 1nj8