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(-) Description

Title :  RHODOPSEUDOMONAS PALUSTRIS PROLYL-TRNA SYNTHETASE IN COMPLEX WITH PROAMS
 
Authors :  T. Crepin, A. Yaremchuk, M. Tukalo, S. Cusack
Date :  22 Aug 06  (Deposition) - 24 Oct 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Alpha Beta, 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 An 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 - PROLINE-TRNA LIGASE
    Chains: A, B, C
    EC Number: 6.1.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21-CODONPLUS-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PROS,RPA2928
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076
    Strain: CGA009-ATCC BAA-98

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1PSD2Ligand/Ion5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PSD1Ligand/Ion5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1PSD2Ligand/Ion5'-O-[N-(PROLYL)-SULFAMOYL]ADENOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:109 , GLU B:111 , ARG B:140 , GLY B:152 , PHE B:155 , MET B:157 , ASP B:159 , TYR B:161 , ILE B:202 , GLU B:282 , VAL B:283 , GLY B:284 , GLN B:285 , PHE B:287 , TYR B:316 , GLY B:317 , GLY B:319 , ARG B:322BINDING SITE FOR RESIDUE PSD B 439
2AC2SOFTWARETHR C:109 , GLU C:111 , ARG C:140 , GLY C:152 , PHE C:155 , MET C:157 , ASP C:159 , TYR C:161 , ILE C:202 , GLU C:282 , VAL C:283 , GLY C:284 , GLN C:285 , PHE C:287 , SER C:315 , TYR C:316 , GLY C:317 , GLY C:319 , ARG C:322BINDING SITE FOR RESIDUE PSD C 439

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2I4M)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:128 -Pro A:129
2Leu B:128 -Pro B:129
3Leu C:128 -Pro C:129

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2I4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2I4M)

(-) Exons   (0, 0)

(no "Exon" information available for 2I4M)

(-) 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:439
 aligned with SYP_RHOPA | Q6N5P6 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:439
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                   
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427         
            SYP_RHOPA     - ---MRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVAR 436
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.............hhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhh..........eeee.....eeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee.......hhhhhh.eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeee..........eeeeeee.....eeeeee.hhhhh............hhhhhhhhhh..eee....hhhhhhhhh....eeeeeeeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeehhhhhhhhhhhhhee..ee..hhhhh...eeeee....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhh..eeeeehhhhhhh.eeeeee.....eeeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i4m A  -2 GSHMRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVAR 436
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427         


Chain B from PDB  Type:PROTEIN  Length:441
 aligned with SYP_RHOPA | Q6N5P6 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:441
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 
            SYP_RHOPA     - ---MRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVARLT 438
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.................hhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhhhhhhhhhhhhhh.eee.....eeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee.......hhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhh...eeeee.........eeeeeeee.....eeeeee.hhhhh............hhhhhhhhhh..eee....hhhhhhh......eeeeeeeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeeehhhhhhhhhhhhee..ee..hhhhh...eeeee....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.......eee...hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i4m B  -2 GSHMRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVARLT 438
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 


Chain C from PDB  Type:PROTEIN  Length:441
 aligned with SYP_RHOPA | Q6N5P6 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:441
                               1                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437 
            SYP_RHOPA     - ---MRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVARLT 438
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhh.............hhhhhhhhhh..eeeee..eeeehhhhhhhhhhhhhhhhhhhhhhh.ee.....eeehhhhhh......hhhhheeee.....eeee...hhhhhhhhhhhhh.hhhhh.eeeeeeeeee.......hhhhh..eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhh....eeeee..........eeeeeee.....eeeeee.hhhhh............hhhhhhhhh...eee....hhhhhhh..hhh.eeeeeeeeeeeeeeeehhhhhhhh.eee.....eee.eeeeeeeehhhhhhhhhhhhee..ee..........eeeee....hhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhh...eeeeehhhhhhh.eeeeee.......eeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i4m C  -2 GSHMRLSRFFLPILKENPKEAEIVSHRLMLRAGMLRQEAAGIYAWLPLGHRVLKKIEQIVREEQNRAGAIELLMPTLQLADLWRESGRYDAYGPEMLRIADRHKRELLYGPTNEEMITEIFRAYIKSYKSLPLNLYHIQWKFRDEQRPRFGVMRGREFLMKDAYSFDVDEAGARKSYNKMFVAYLRTFARMGLKAIPMRAETGPIGGDLSHEFIVLAETGESGVYIDRDVLNLPVPDENVDYDGDLTPIIKQWTSVYAATEDVHEPARYESEVPEANRLNTRGIEVGQIFYFGTKYSDSMKANVTGPDGTDAPIHGGSYGVGVSRLLGAIIEACHDDNGIIWPEAVAPFRVTILNLKQGDAATDAACDQLYRELSAKGVDVLYDDTDQRAGAKFATADLIGIPWQIHVGPRGLAEGKVELKRRSDGARENLALADVVARLT 438
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
   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 2I4M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2I4M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2I4M)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SYP_RHOPA | Q6N5P6)
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: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: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

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        SYP_RHOPA | Q6N5P6: 2i4l 2i4n 2i4o

(-) Related Entries Specified in the PDB File

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