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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN CYTOSOLIC HISTIDYL-TRNA SYNTHETASE, HISTIDINE-BOUND
 
Authors :  C. Y. Koh, A. B. Wetzel, W. J. De Van Der Schueren, W. G. J. Hol
Date :  06 May 14  (Deposition) - 27 Aug 14  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.84
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Aminoacyl-Trna Synthetase, Aars, Hisrs, Human, Cytoplasmic, Ligase, Protein-Substrate Complex, Rossmann-Fold, Translation, Nucleotide Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Y. Koh, A. B. Wetzel, W. J. De Van Der Schueren, W. G. Hol
Comparison Of Histidine Recognition In Human And Trypanosomatid Histidyl-Trna Synthetases.
Biochimie V. 106 111 2014
PubMed-ID: 25151410  |  Reference-DOI: 10.1016/J.BIOCHI.2014.08.005

(-) Compounds

Molecule 1 - HISTIDINE--TRNA LIGASE, CYTOPLASMIC
    Chains: A, B, C, D
    EC Number: 6.1.1.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HARS, HRS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTIDYL-TRNA SYNTHETASE,HISRS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2HIS4Mod. Amino AcidHISTIDINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HIS2Mod. Amino AcidHISTIDINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2HIS2Mod. Amino AcidHISTIDINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:130 , THR A:132 , ARG A:157 , GLN A:173 , ASP A:175 , ASP A:177 , ARG A:326 , LEU A:328 , TYR A:330 , TYR A:331 , GLY A:360 , TYR A:363 , GLY A:381 , LEU A:382 , SER A:383 , HOH A:1113binding site for residue HIS A 1001
2AC2SOFTWAREASN A:146 , TYR B:454binding site for residue GOL A 1002
3AC3SOFTWAREASP B:130 , THR B:132 , ARG B:157 , GLN B:173 , ASP B:175 , ASP B:177 , ARG B:326 , TYR B:330 , TYR B:331 , GLY B:360 , TYR B:363 , GLY B:381 , LEU B:382 , HOH B:1116binding site for residue HIS B 1001
4AC4SOFTWARETYR A:454 , ASN B:146binding site for residue GOL B 1002
5AC5SOFTWAREASP C:130 , THR C:132 , ARG C:157 , GLN C:173 , ASP C:175 , ASP C:177 , ARG C:326 , LEU C:328 , TYR C:330 , TYR C:331 , TYR C:363 , GLY C:381 , LEU C:382binding site for residue HIS C 1001
6AC6SOFTWAREASN C:146 , TYR D:454binding site for residue GOL C 1002
7AC7SOFTWARETYR C:454 , GLU D:90 , ASN D:146binding site for residue GOL C 1003
8AC8SOFTWAREASP D:130 , THR D:132 , ARG D:157 , GLN D:173 , ASP D:175 , ASP D:177 , ARG D:326 , TYR D:330 , TYR D:331 , GLY D:360 , GLY D:381 , LEU D:382 , SER D:383 , HOH D:1109binding site for residue HIS D 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PHC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PHC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PHC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PHC)

(-) Exons   (0, 0)

(no "Exon" information available for 4PHC)

(-) 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:445
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh...hhhhhhh..........eee...hhhhhhhhhhhh....eeeeeeeeee.............eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeee........eeeeeeee..hhhhhhh.......eeeeeeehhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4phc A   53 KFVLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNPAMTRGRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQTEPLGVGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQH 1001
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342||     358       368       378       388       398 ||    410       420       430       440       450       460       470       480       490       500   ||
                                                                                                                                                                                                                                                                                                                            343|                                               400|                                                                                                  504|
                                                                                                                                                                                                                                                                                                                             350                                                403                                                                                                  1001


Chain B from PDB  Type:PROTEIN  Length:442
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh...hhhhhhh..........eee...hhhhhhhhhhhhh...eeeeeeeeee.............eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeee........eeeee..hhhhhhh.......eeeeeeehhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4phc B   53 KFVLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNPAMTRGRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQTPAQSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQH 1001
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342   ||  361       371       381       391       403       413       423       433       443       453       463       473       483       493       503||
                                                                                                                                                                                                                                                                                                                               346|                                         400|                                                                                                  504|
                                                                                                                                                                                                                                                                                                                                356                                          403                                                                                                  1001


Chain C from PDB  Type:PROTEIN  Length:441
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh...hhhhhhh..........eee...hhhhhhhhhhhhh...eeeeeeeeee.............eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeee.......eeeee..hhhhhhh.......eeeeeeehhhhhhhhhhhhhhh........eeeee....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4phc C   53 KFVLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNPAMTRGRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQTPGSVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQH 1001
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342 ||    362       372       382       392       404       414       424       434       444       454       464       474       484       494       504|
                                                                                                                                                                                                                                                                                                                             344|                                          400|                                                                                                  504|
                                                                                                                                                                                                                                                                                                                              355                                           403                                                                                                  1001


Chain D from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhh..ee.....eeehhhhh...hhhhhhh..........eee...hhhhhhhhhhhhh...eeeeeeeeee.............eeeeeeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhhhhhh.eehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeee............eeeeeee.......eeeee..hhhhhhh.......eeeeeeehhhhhhhhhhhhhhh..........eeeee....hhhhhhhhhhhhhhh...ee.......hhhhhhhhhhhhh..eeeeehhhhhhhheeeeee.....eeeee..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4phc D   53 KFVLKTPKGTRDYSPRQMAVREKVFDVIIRCFKRHGAEVIDTPVFELKETLMGKYGEDSKLIYDLKDQGGELLSLRYDLTVPFARYLAMNKLTNIKRYHIAKVYRRDNPAMTRGRYREFYQCDFDIAGNFDPMIPDAECLKIMCEILSSLQIGDFLVKVNDRRILDGMFAICGVSDSKFRTICSSVDKLDKVSWEEVKNEMVGEKGLAPEVADRIGDYVQQHGGVSLVEQLLQDPKLSQNKQALEGLGDLKLLFEYLTLFGIDDKISFDLSLARGLDYYTGVIYEAVLLQTPASVAAGGRYDGLVGMFDPKGRKVPCVGLSIGVERIFSIVEQRLEALEEKIRTTETQVLVASAQKKLLEERLKLVSELWDAGIKAELLYKKNPKLLNQLQYCEEAGIPLVAIIGEQELKDGVIKLRSVTSREEVDVRREDLVEEIKRRTGQH 1001
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342  ||   362       372       382       392       402       412       422       432       442       452       462       472       482       492       502 ||
                                                                                                                                                                                                                                                                                                                              345|                                                                                                                                                 504|
                                                                                                                                                                                                                                                                                                                               356                                                                                                                                                 1001
   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 4PHC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PHC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PHC)

(-) Gene Ontology  (12, 12)

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        SYHC_HUMAN | P12081: 1x59 2lw7 4g84 4g85 4x5o

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