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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN (APO STRUCTURE)
 
Authors :  A. Palencia, R. J. Liu, M. Lukarska, J. Gut, A. Bougdour, B. Touquet, E. D M. R. K. Alley, P. J. Rosenthal, M. A. Hakimi, S. Cusack
Date :  24 Nov 15  (Deposition) - 03 Aug 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Ligase, Cryptosporidium, Leucine-Trna Ligase (Leurs) Activity, Atp + L-Leucine + Trna(Leucine) Give Amp + Diphosphate + L- Leucyl-Trna(Leucine), Post-Transfer Editing Activity Of Leurs, Aminoacyl-Trna Synthetase, Protein Biosynthesis, Novel Boron Inhibitors Of The Editing Site Of Leurs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Palencia, R. Liu, M. Lukarska, J. Gut, A. Bougdour, B. Touquet, E. Wang, X. Li, M. R. K. Alley, Y. R. Freund, P. J. Rosenthal, M. Hakimi, S. Cusack
Cryptosporidium And Toxoplasma Parasites Are Inhibited By A Benzoxaborole Targeting Leucyl-Trna Synthetase.
Antimicrob. Agents Chemother. V. 60 5817 2016
PubMed-ID: 27431220  |  Reference-DOI: 10.1128/AAC.00873-16

(-) Compounds

Molecule 1 - LEUCYL-TRNA SYNTHETASE
    Chains: A, C, D
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector: PETM-11
    Expression System Vector Type: PLASMID
    Fragment: EDITING DOMAIN
    Organism Scientific: CRYPTOSPORIDIUM MURIS
    Organism Taxid: 441375
    Strain: RN66
 
Molecule 2 - LEUCYL-TRNA SYNTHETASE
    Chains: B
    EC Number: 6.1.1.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIL
    Expression System Vector: PETM-11
    Expression System Vector Type: PLASMID
    Fragment: EDITING DOMAIN
    Organism Scientific: CRYPTOSPORIDIUM MURIS
    Organism Taxid: 441375
    Strain: RN66

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5FON)

(-) Sites  (0, 0)

(no "Site" information available for 5FON)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FON)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FON)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FON)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FON)

(-) Exons   (0, 0)

(no "Exon" information available for 5FON)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee............ee.hhhhhh....eeeeehhhhhhhhhh.....eeeee.......eeee..eeeeee.hhhh..eee.......eeeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fon A 255 PQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPDGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHGREQGVSDKLLPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   264       274       284       294       304       314   ||  330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540 
                                                                                         318|                                                                                                                                                                                                                        
                                                                                          325                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee..............hhhhhh..eeeeehhhhhhhhhh............eeeeeehhhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhhh.hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fon B 255 PQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQEGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   264       274       284       294       304       314||     333       343       353       363  ||   384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       
                                                                                      315|                                      366|                                                                                                                                                                   
                                                                                       325                                       378                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee.......ee.hhhhhhhh..eeeeehhhhhhhhhh.....ee..ee.eeeeee.hhhh..eee.......eeeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhh..ee.hhhhh..hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fon C 256 QEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIHPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   265       275       285       295       305       315|      336       346       356       366|      387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537    
                                                                                     315|                                    366|                                                                                                                                                                   
                                                                                      327                                     378                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee...hhhhhhhhh..eeeeeeee.hhhhhhhh.eeee....eeeeeee.................hhhhhhh...eeeeehhhhhhhhhh...........eeeeee.hhhh..eee........eeeee...........eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh......ee......hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fon D 255 PQEYTLIKLKIHLIPEFLGSIVKGREVFVVCATLRPETMYGQTNCWILPDGEYDLVLAFDQVIPYDDGVLCKIFDKYEDTMKECNTVYICSERSAYNMAYQGIVPLIPRIVSLGKVYGEQLIGTPLSAPMTPYSLIFILPMFSISMEKGTGIVTSVPSDSPDDYAALRDIKTKPLLREKYSIKDEWILDPLEIIEVPGFGFMTAELLCNQYKIQSQNDSAKLKQAKEEIYKKEFYEGILIRGKYSGMKICDAKELIRESLIKDGYALIYLE 541
                                   264       274       284       294       304       314     ||328       338       348       358      |380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540 
                                                                                           320|                                     365|                                                                                                                                                                   
                                                                                            325                                      378
   Legend:   → Mismatch (orange background)
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  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 5FON)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FON)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FON)

(-) Gene Ontology  (11, 11)

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 Related Entries

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        B6AA20_CRYMR | B6AA20: 5fog 5fol 5fom

(-) Related Entries Specified in the PDB File

5fo4 CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1)
5foc CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P21)
5fod CRYSTAL STRUCTURE OF THE P.FALCIPARUM CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN (SPACE GROUP P1) CONTAINING DELETIONS OF INSERTIONS 1 AND 3
5fof CRYSTAL STRUCTURE OF THE P.KNOWLESI CYTOSOLIC LEUCYL- TRNA SYNTHETASE EDITING DOMAIN
5fog CRYSTAL STRUCTURE OF HTE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH A POST-TRANSFER EDITING ANALOGUE OF NORVALINE (NV2AA)
5fol CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH A POST-TRANSFER EDITING ANALOGUE OF ISOEUCINE (ILE2AA)
5fom CRYSTAL STRUCTURE OF THE CRYPTOSPORIDIUM MURIS CYTOSOLIC LEUCYL-TRNA SYNTHETASE EDITING DOMAIN COMPLEX WITH THE ADDUCT AMP-AN6426