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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN AMINOACYL-TRNA SYNTHETASE CYTOKINE
 
Authors :  X. -L. Yang, R. J. Skene, D. E. Mcree, P. Schimmel
Date :  28 Oct 02  (Deposition) - 20 Nov 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rossmann Fold As Catalytic Domain, Unique Anticodon Recognition Domain, Dimer, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. -L. Yang, R. J. Skene, D. E. Mcree, P. Schimmel
Crystal Structure Of A Human Aminoacyl-Trna Synthetase Cytokine
Proc. Natl. Acad. Sci. Usa V. 99 15369 2002
PubMed-ID: 12427973  |  Reference-DOI: 10.1073/PNAS.242611799

(-) Compounds

Molecule 1 - TYROSYL-TRNA SYNTHETASE
    ChainsA
    EC Number6.1.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentMINI TYRRS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO48Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:49 , VAL A:50 , ALA A:51 , GLY A:217 , LEU A:218 , THR A:219 , LYS A:231 , HOH A:2010 , HOH A:2033 , HOH A:2035BINDING SITE FOR RESIDUE SO4 A 501
2AC2SOFTWAREHIS A:305 , PRO A:306 , GLY A:307 , ASP A:308 , HOH A:2199 , HOH A:2211BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARELYS A:26 , ARG A:34 , HOH A:2066 , HOH A:2230BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWARELYS A:282 , TRP A:283 , HOH A:2040 , HOH A:2294BINDING SITE FOR RESIDUE SO4 A 504
5AC5SOFTWAREMET A:214 , PRO A:216 , SER A:262 , LYS A:265 , HIS A:266 , HOH A:2086 , HOH A:2101 , HOH A:2146 , HOH A:2223BINDING SITE FOR RESIDUE GOL A 601
6AC6SOFTWAREHIS A:12 , ARG A:16 , SER A:273BINDING SITE FOR RESIDUE GOL A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N3L)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:4 -Pro A:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026681G41RSYYC_HUMANDisease (CMTDIC)121908833AG41R
2UniProtVAR_026683Q170HSYYC_HUMANPolymorphism2128600AQ170H
3UniProtVAR_026684E196KSYYC_HUMANDisease (CMTDIC)121908834AE196K
4UniProtVAR_073292E274KSYYC_HUMANUnclassified758897498AE274K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026681G41RSYYC_HUMANDisease (CMTDIC)121908833AG41R
2UniProtVAR_026683Q170HSYYC_HUMANPolymorphism2128600AQ170H
3UniProtVAR_026684E196KSYYC_HUMANDisease (CMTDIC)121908834AE196K
4UniProtVAR_073292E274KSYYC_HUMANUnclassified758897498AE274K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N3L)

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003734771aENSE00001460665chr1:33283754-33282789966SYYC_HUMAN1-19191A:4-1916
1.2bENST000003734772bENSE00001208748chr1:33276658-33276512147SYYC_HUMAN20-68491A:20-6849
1.3bENST000003734773bENSE00001208739chr1:33276367-33276192176SYYC_HUMAN69-127591A:69-12759
1.4aENST000003734774aENSE00001208728chr1:33272212-33272083130SYYC_HUMAN127-170441A:127-17044
1.5bENST000003734775bENSE00001208722chr1:33263444-3326336481SYYC_HUMAN171-197271A:171-19727
1.7aENST000003734777aENSE00001208715chr1:33256855-3325676393SYYC_HUMAN198-228311A:198-22124
1.8ENST000003734778ENSE00000916656chr1:33252676-33252541136SYYC_HUMAN229-274461A:229-27446
1.9cENST000003734779cENSE00000916655chr1:33252048-3325196386SYYC_HUMAN274-302291A:274-30229
1.10bENST0000037347710bENSE00001065998chr1:33248140-33248005136SYYC_HUMAN303-348461A:303-34240
1.11bENST0000037347711bENSE00001065997chr1:33246746-3324664998SYYC_HUMAN348-380330--
1.12bENST0000037347712bENSE00001168511chr1:33245879-33245686194SYYC_HUMAN381-445650--
1.12cENST0000037347712cENSE00001065999chr1:33245124-33244983142SYYC_HUMAN445-492480--
1.13dENST0000037347713dENSE00001460663chr1:33241692-33240840853SYYC_HUMAN493-528360--

(-) 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:332
 aligned with SYYC_HUMAN | P54577 from UniProtKB/Swiss-Prot  Length:528

    Alignment length:339
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333         
           SYYC_HUMAN     4 APSPEEKLHLITRNLQEVLGEEKLKEILKERELKIYWGTATTGKPHVAYFVPMSKIADFLKAGCEVTILFADLHAYLDNMKAPWELLELRVSYYENVIKAMLESIGVPLEKLKFIKGTDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEYLKVDAQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGSKMSSSEEESKIDLLDRKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYP 342
               SCOP domains d1n3la_ A: Tyrosyl-tRNA synthetase (TyrRS)                                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains -1n3lA01 A:5-213 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                                            ---1n3lA       02 A:217-342 Tyrosyl-Transfer RNA Synthetase                                                                       CATH domains
               Pfam domains ---------------------------tRNA-synt_1b-1n3lA01 A:31-322                                                                                                                                                                                                                                                                       -------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeehhhhhhhhhh....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhh..hhhhhhhhhhhhh..hhhhhhhhh..........hhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh....eeeee.........-------........hhhhhhhhhhh..........hhhhhhhhhh.......eee..hhhhh..eee.hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------R--------------------------------------------------------------------------------------------------------------------------------H-------------------------K-----------------------------------------------------------------------------K-------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a       Exon 1.2b  PDB: A:20-68 UniProt: 20-68           Exon 1.3b  PDB: A:69-127 UniProt: 69-127                   -------------------------------------------Exon 1.5b  PDB: A:171-197  Exon 1.7a  PDB: A:198-221      Exon 1.8  PDB: A:229-274 UniProt: 229-274     ----------------------------Exon 1.10b  PDB: A:303-342 [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.4a  PDB: A:127-170 UniProt: 127-170  -------------------------------------------------------------------------------------------------------Exon 1.9c  PDB: A:274-302    ---------------------------------------- Transcript 1 (2)
                 1n3l A   4 APSPEEKLHLITRNLQEVLGEEKLKEILKERELKIYWGTATTGKPHVAYFVPMSKIADFLKAGCEVTILFADLHAYLDNMKAPWELLELRVSYYENVIKAMLESIGVPLEKLKFIKGTDYQLSKEYTLDVYRLSSVVTQHDSKKAGAEVVKQVEHPLLSGLLYPGLQALDEEYLKVDAQFGGIDQRKIFTFAEKYLPALGYSKRVHLMNPMVPGLTGS-------ESKIDLLDRKEDVKKKLKKAFCEPGNVENNGVLSFIKHVLFPLKSEFVILRDEKWGGNKTYTAYVDLEKDFAAEVVHPGDLKNSVEVALNKLLDPIREKFNTPALKKLASAAYP 342
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       | -     | 233       243       253       263       273       283       293       303       313       323       333         
                                                                                                                                                                                                                                                   221     229                                                                                                                 

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: HUP (230)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (SYYC_HUMAN | P54577)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0005153    interleukin-8 receptor binding    Interacting selectively and non-covalently with the interleukin-8 receptor.
    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: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).
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0004831    tyrosine-tRNA ligase activity    Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H(+).
    GO:0004832    valine-tRNA ligase activity    Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H(+).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    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.
    GO:0006437    tyrosyl-tRNA aminoacylation    The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-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:0006438    valyl-tRNA aminoacylation    The process of coupling valine to valyl-tRNA, catalyzed by valyl-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.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SYYC_HUMAN | P545771ntg 1q11 4q93 4qbt 5thh 5thl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1N3L)