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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTEINYL-TRNA SYNTHETASE BINARY COMPLEX WITH TRNACYS
 
Authors :  S. Hauenstein, C. M. Zhang, Y. M. Hou, J. J. Perona
Date :  13 Jul 04  (Deposition) - 23 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Hauenstein, C. M. Zhang, Y. M. Hou, J. J. Perona
Shape-Selective Rna Recognition By Cysteinyl-Trna Synthetase
Nat. Struct. Mol. Biol. V. 11 1134 2004
PubMed-ID: 15489861  |  Reference-DOI: 10.1038/NSMB849
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINYL-TRNA SYNTHETASE
    Chains: A
    EC Number: 6.1.1.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK107
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYSS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CYSTEINE--TRNA LIGASE, CYSRS
 
Molecule 2 - CYSTEINYL TRNA
    Chains: B
    Engineered: YES
    Other Details: T7 TRANSCRIPTION
    Synonym: TRNACYS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:28 , CYS B:209 , HIS B:234 , GLU B:238BINDING SITE FOR RESIDUE ZN B 462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U0B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U0B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U0B)

(-) Exons   (0, 0)

(no "Exon" information available for 1U0B)

(-) 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:RNA  Length:74
                                                                                                          
                 1u0b A   1 GGCGCGUUAACAAAGCGGUUAUGUAGCGGAUUGCAAAUCCGUCUAGUCCGGUUCGACUCCGGAACGCGCCUCCA  76
                                    10     || 21        31        41    ||  52        62        72    
                                          16|                          46|                            
                                           18                           48                            


Chain B from PDB  Type:PROTEIN  Length:461
 aligned with SYC_ECOLI | P21888 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:461
                                    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 
            SYC_ECOLI     1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQDLDQLQAGARVDVVDDKRNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFLQSGAQADDSEVAEIEALIQQRLDARKAKDWAAADAARDRLNEMGIVLEDGPQGTTWRRK 461
               SCOP domains d1u0bb2 B:1-315 Cysteinyl-tRNA synthetase (CysRS)                                                                                                                                                                                                                                                                          d1u0bb1 B:316-461 Cysteinyl-tRNA synthetase (CysRS)                                                                                                SCOP domains
               CATH domains 1u0bB01 B:1-305 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                                                                                                                            ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------tRNA-synt_1e-1u0bB02 B:14-314                                                                                                                                                                                                                                                                                --------------------------DALR_2-1u0bB01 B:341-402                                      ----------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee......eee.......eeeeee.........hhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhh..eee.....eee.hhhh.........hhhhhhhh..............eeeeee..............ee...hhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhhhhhhhhh....eeeeeee..eee..ee.........hhhhhh...hhhhhhhhhh.......ee.hhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u0b B   1 MLKIFNTLTRQKEEFKPIHAGEVGMYVCGITVYDLCHIGHGRTFVAFDVVARYLRFLGYKLKYVRNITDIDDKIIKRANENGESFVAMVDRMIAEMHKDFDALNILRPDMEPRATHHIAEIIELTEQLIAKGHAYVADNGDVMFDVPTDPTYGVLSRQDLDQLQAGARVDVVDDKRNPMDFVLWKMSKEGEPSWPSPWGAGRPGWHIECSAMNCKQLGNHFDIHGGGSDLMFPHHENEIAQSTCAHDGQYVNYWMHSGMVMVDREKMSKSLGNFFTVRDVLKYYDAETVRYFLMSGHYRSQLNYSEENLKQARAALERLYTALRGTDKTVAPAGGEAFEARFIEAMDDDFNTPEAYSVLFDMAREVNRLKAEDMAAANAMASHLRKLSAVLGLLEQEPEAFLQSGAQADDSEVAEIEALIQQRLDARKAKDWAAADAARDRLNEMGIVLEDGPQGTTWRRK 461
                                    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
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: DALR (5)
(-)
Clan: HUP (230)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain B   (SYC_ECOLI | P21888)
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:0004817    cysteine-tRNA ligase activity    Catalysis of the reaction: ATP + L-cysteine + tRNA(Cys) = AMP + diphosphate + L-cysteinyl-tRNA(Cys).
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006423    cysteinyl-tRNA aminoacylation    The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-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.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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UniProtKB/Swiss-Prot
        SYC_ECOLI | P21888: 1li5 1li7

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