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(-) Description

Title :  PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH A PROLYL-ADENYLATE ANALOGUE ('5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE)
 
Authors :  T. Crepin, A. Yaremchuk, M. Tukalo, S. Cusack
Date :  22 Aug 06  (Deposition) - 11 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacterial-Type Prolyl-Trna Synthetase, Class Ii Aminoacyl- Trna Synthetase, Editing, Translation, Atp + L-Proline + Trna (Pro) Gives Amp + Ppi + L-Prolyl-Trna(Pro), Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Crepin, A. Yaremchuk, M. Tukalo, S. Cusack
Structures Of Two Bacterial Prolyl-Trna Synthetases With And Without A Cis-Editing Domain.
Structure V. 14 1511 2006
PubMed-ID: 17027500  |  Reference-DOI: 10.1016/J.STR.2006.08.007

(-) Compounds

Molecule 1 - PROLYL-TRNA SYNTHETASE
    Chains: A, B
    EC Number: 6.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-60
    Expression System Strain: M15
    Expression System Taxid: 562
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1P5A2Ligand/Ion'5'-O-(N-(L-PROLYL)-SULFAMOYL)ADENOSINE
2SO421Ligand/IonSULFATE ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:272 , GLU A:273 , ARG A:276 , HIS B:246BINDING SITE FOR RESIDUE SO4 A1566
02AC2SOFTWAREARG A:151 , ASP A:219 , ARG A:447 , HOH A:2045BINDING SITE FOR RESIDUE SO4 A1567
03AC3SOFTWAREASN A:123 , SER A:124 , ARG A:127BINDING SITE FOR RESIDUE SO4 A1568
04AC4SOFTWARETHR A:88 , GLY A:203 , ARG A:417 , HOH A:2042 , HOH A:2083BINDING SITE FOR RESIDUE SO4 A1569
05AC5SOFTWARETHR A:262 , ILE A:263BINDING SITE FOR RESIDUE SO4 A1570
06AC6SOFTWARELYS A:243 , ARG A:295BINDING SITE FOR RESIDUE SO4 A1571
07AC7SOFTWARELYS A:244 , HIS A:246 , GLU A:247 , SER B:245 , HIS B:246BINDING SITE FOR RESIDUE SO4 A1572
08AC8SOFTWAREARG A:193 , ALA A:194BINDING SITE FOR RESIDUE SO4 A1573
09AC9SOFTWARELYS A:205 , ASP A:420 , LYS A:434 , SER A:435 , HOH A:2071BINDING SITE FOR RESIDUE SO4 A1574
10BC1SOFTWAREARG A:99BINDING SITE FOR RESIDUE SO4 A1575
11BC2SOFTWARETHR B:262 , ILE B:263 , LYS B:279 , HOH B:2118BINDING SITE FOR RESIDUE SO4 B1571
12BC3SOFTWARELYS A:244 , HIS A:246 , VAL B:272 , GLU B:273 , ARG B:276BINDING SITE FOR RESIDUE SO4 B1572
13BC4SOFTWAREARG B:151 , GLU B:218 , ASP B:219 , ARG B:447 , HOH B:2119BINDING SITE FOR RESIDUE SO4 B1573
14BC5SOFTWAREILE B:122 , ASN B:123 , SER B:124 , ARG B:127BINDING SITE FOR RESIDUE SO4 B1574
15BC6SOFTWARETHR B:88 , GLY B:203 , ARG B:417 , HOH B:2050BINDING SITE FOR RESIDUE SO4 B1575
16BC7SOFTWAREARG A:324 , ASP B:166 , GLU B:167 , LYS B:434BINDING SITE FOR RESIDUE SO4 B1576
17BC8SOFTWAREARG B:193 , ALA B:194BINDING SITE FOR RESIDUE SO4 B1577
18BC9SOFTWAREGLU B:167 , LYS B:205 , GLY B:415 , THR B:416BINDING SITE FOR RESIDUE SO4 B1578
19CC1SOFTWAREARG B:48 , GLU B:502BINDING SITE FOR RESIDUE SO4 B1579
20CC2SOFTWAREARG B:144 , ARG B:151BINDING SITE FOR RESIDUE SO4 B1580
21CC3SOFTWARELYS B:243 , ARG B:295BINDING SITE FOR RESIDUE SO4 B1581
22CC4SOFTWARETHR A:109 , GLU A:111 , ARG A:140 , GLU A:142 , GLY A:152 , PHE A:155 , MET A:157 , ASP A:159 , TYR A:161 , GLU A:407 , ILE A:408 , GLY A:409 , HIS A:410 , PHE A:412 , TYR A:441 , GLY A:442 , GLY A:444 , ARG A:447 , HOH A:2030 , HOH A:2084BINDING SITE FOR RESIDUE P5A A1576
23CC5SOFTWARETHR B:109 , GLU B:111 , ARG B:140 , GLU B:142 , GLY B:152 , PHE B:155 , MET B:157 , ASP B:159 , TYR B:161 , MET B:202 , GLU B:407 , ILE B:408 , GLY B:409 , HIS B:410 , PHE B:412 , TYR B:441 , GLY B:442 , GLY B:444 , ARG B:447 , HOH B:2044BINDING SITE FOR RESIDUE P5A B1582

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J3L)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:128 -Pro A:129
2Leu B:128 -Pro B:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J3L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J3L)

(-) Exons   (0, 0)

(no "Exon" information available for 2J3L)

(-) Sequences/Alignments

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:565
 aligned with SYP_ENTFA | Q831W7 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:565
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     
            SYP_ENTFA     1 MKQSKMLIPTLREVPNDAEVLSHQILLRAGYIRQVAAGIYSYLPLANRVLEKLKTIMREEFEKIDAVEMLMPALLPAELWKESGRYETYGPNLYRLKDRNDRDYILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAIIGDGGAMGGKDSKEFMAISEIGEDTICYSTESDYAANLEMATSLYTPKKSHETQLDLEKIATPEVGTIAEVANFFEVEPQRIIKSVLFIADEEPVMVLVRGDHDVNDVKLKNFLGADFLDEATEEDARRVLGAGFGSIGPVNVSEDVKIYADLAVQDLANAIVGANEDGYHLTNVNPDRDFQPISYEDLRFVQEGDPSPDGNGVLAFTKGIEIGHIFKLGTRYSDAMGATVLDENGREKSVIMGCYGIGVSRLLSAIVEQNADERGINWPTGIAPFDLHVVQMNVKDEYQTKLSQEVEAMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITVGKKAVDGVVEVKIKRTGEMLEVRKEELESTLSILM 565
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhh.............hhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh.....eee.....eeee...hhhhhhhhhhhhh..hhhh.eeeeeeeeee.......hhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...eeeeeee.....eeeeee.....eee....................eeee.....hhhhhhhhhh.hhhh.eeeeeeee..eeeeeeee.....hhhhhhhhhh...eee.hhhhhhhhhh...............eeeee........eeee.....eeeeee.........eee.................eeeeeeeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeeehhhhhhhhhhhhee..ee..........eeeee....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeeehhhhhh.eeeeee.....eeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j3l A   1 MKQSKMLIPTLREVPNDAEVLSHQILLRAGYIRQVAAGIYSYLPLANRVLEKLKTIMREEFEKIDAVEMLMPALLPAELWKESGRYETYGPNLYRLKDRNDRDYILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAIIGDGGAMGGKDSKEFMAISEIGEDTICYSTESDYAANLEMATSLYTPKKSHETQLDLEKIATPEVGTIAEVANFFEVEPQRIIKSVLFIADEEPVMVLVRGDHDVNDVKLKNFLGADFLDEATEEDARRVLGAGFGSIGPVNVSEDVKIYADLAVQDLANAIVGANEDGYHLTNVNPDRDFQPISYEDLRFVQEGDPSPDGNGVLAFTKGIEIGHIFKLGTRYSDAMGATVLDENGREKSVIMGCYGIGVSRLLSAIVEQNADERGINWPTGIAPFDLHVVQMNVKDEYQTKLSQEVEAMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITVGKKAVDGVVEVKIKRTGEMLEVRKEELESTLSILM 565
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560     


Chain B from PDB  Type:PROTEIN  Length:570
 aligned with SYP_ENTFA | Q831W7 from UniProtKB/Swiss-Prot  Length:572

    Alignment length:570
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570
            SYP_ENTFA     1 MKQSKMLIPTLREVPNDAEVLSHQILLRAGYIRQVAAGIYSYLPLANRVLEKLKTIMREEFEKIDAVEMLMPALLPAELWKESGRYETYGPNLYRLKDRNDRDYILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAIIGDGGAMGGKDSKEFMAISEIGEDTICYSTESDYAANLEMATSLYTPKKSHETQLDLEKIATPEVGTIAEVANFFEVEPQRIIKSVLFIADEEPVMVLVRGDHDVNDVKLKNFLGADFLDEATEEDARRVLGAGFGSIGPVNVSEDVKIYADLAVQDLANAIVGANEDGYHLTNVNPDRDFQPISYEDLRFVQEGDPSPDGNGVLAFTKGIEIGHIFKLGTRYSDAMGATVLDENGREKSVIMGCYGIGVSRLLSAIVEQNADERGINWPTGIAPFDLHVVQMNVKDEYQTKLSQEVEAMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITVGKKAVDGVVEVKIKRTGEMLEVRKEELESTLSILMNTTSE 570
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhh.............hhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhhhh...ee.....eeehhhhhhhhhhhhh.....eee.....eeee...hhhhhhhhhhhhh..hhhh.eeeeeeeeee.......hhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhh...eeeeeee.....eeeeee.....eee....................eeee.....hhhhhhhhh..hhhh.eeeeeeee..eeeeeeee.....hhhhhhhhhh...eee.hhhhhhhhhh.hhhhh.........eeeee.hhhhh..eeee.....eeeeee.........eee.................eeeeeeeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeeehhhhhhhhhhhhee..ee..........eeeee....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeeehhhhhh.eeeeee.....eeeee..hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2j3l B   1 MKQSKMLIPTLREVPNDAEVLSHQILLRAGYIRQVAAGIYSYLPLANRVLEKLKTIMREEFEKIDAVEMLMPALLPAELWKESGRYETYGPNLYRLKDRNDRDYILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLRGREFIMKDGYSFHADEASLDQSYRDYEKAYSRIFERCGLEFRAIIGDGGAMGGKDSKEFMAISEIGEDTICYSTESDYAANLEMATSLYTPKKSHETQLDLEKIATPEVGTIAEVANFFEVEPQRIIKSVLFIADEEPVMVLVRGDHDVNDVKLKNFLGADFLDEATEEDARRVLGAGFGSIGPVNVSEDVKIYADLAVQDLANAIVGANEDGYHLTNVNPDRDFQPISYEDLRFVQEGDPSPDGNGVLAFTKGIEIGHIFKLGTRYSDAMGATVLDENGREKSVIMGCYGIGVSRLLSAIVEQNADERGINWPTGIAPFDLHVVQMNVKDEYQTKLSQEVEAMMTEAGYEVLVDDRNERAGVKFADADLIGCPIRITVGKKAVDGVVEVKIKRTGEMLEVRKEELESTLSILMNTTSE 570
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570
   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  (0, 0)

(no "SCOP Domain" information available for 2J3L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2J3L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J3L)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (SYP_ENTFA | Q831W7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0002161    aminoacyl-tRNA editing activity    The hydrolysis of an incorrectly aminoacylated tRNA.
    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: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).
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:0006450    regulation of translational fidelity    Any process that modulates the ability of the translational apparatus to interpret the genetic code.
    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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        SYP_ENTFA | Q831W7: 2j3m

(-) Related Entries Specified in the PDB File

2j3m PROLYL-TRNA SYNTHETASE FROM ENTEROCOCCUS FAECALIS COMPLEXED WITH ATP, MANGANESE AND PROLINOL