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(-) Description

Title :  CRYSTAL STRUCTURE WLARD, A SUGAR 3N-FORMYL TRANSFERASE IN THE PRESENCE OF DTDP-GLC AND 10-N-FORMYL-THF
 
Authors :  J. B. Thoden, M. -F. Goneau, M. Gilbert, H. M. Holden
Date :  30 Jul 13  (Deposition) - 14 Aug 13  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Formyltransferase, Formylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Thoden, M. F. Goneau, M. Gilbert, H. M. Holden
Structure Of A Sugar N-Formyltransferase From Campylobacter Jejuni.
Biochemistry V. 52 6114 2013
PubMed-ID: 23898784  |  Reference-DOI: 10.1021/BI4009006

(-) Compounds

Molecule 1 - WLARD, A SUGAR 3N-FORMYL TRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA2(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: C8J_1081
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 407148
    Strain: 81116

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
11YA2Ligand/IonN-{4-[{[(6S)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}(FORMYL)AMINO]BENZOYL}-L-GLUTAMIC ACID
2DAU2Ligand/Ion2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:75 , PHE A:78 , ASP A:79 , GLN A:80 , ILE A:81 , ILE A:82 , ASN A:94 , VAL A:106 , HIS A:125 , ILE A:127 , ASP A:128 , GLY A:130 , ASP A:132 , SER A:191 , ARG A:192 , DAU A:302 , HOH A:404 , HOH A:410 , HOH A:450 , HOH A:653 , HOH A:767 , LYS B:204 , HOH B:687BINDING SITE FOR RESIDUE 1YA A 301
2AC2SOFTWARELYS A:9 , ASN A:35 , GLU A:77 , PHE A:78 , ASP A:79 , VAL A:106 , PHE A:107 , THR A:108 , SER A:109 , TYR A:154 , ARG A:192 , LEU A:197 , PHE A:219 , TYR A:222 , GLN A:223 , 1YA A:301 , HOH A:409 , HOH A:429 , HOH A:450 , HOH A:469 , HOH A:576 , HOH A:615 , HOH A:652 , HOH A:700 , HOH A:742BINDING SITE FOR RESIDUE DAU A 302
3AC3SOFTWAREPHE A:203 , ILE A:227 , ASN A:228 , HOH A:528 , HOH A:541 , HOH A:709 , HOH A:743BINDING SITE FOR RESIDUE MPO A 303
4AC4SOFTWAREASP A:194 , ILE A:195 , ASN A:196 , HIS A:199 , HOH A:697 , HOH A:755 , HOH A:802BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWARESER B:75 , PHE B:78 , ASP B:79 , GLN B:80 , ILE B:81 , ILE B:82 , ASN B:94 , HIS B:125 , ILE B:127 , ASP B:128 , GLY B:130 , ASP B:132 , DAU B:302 , HOH B:405 , HOH B:408 , HOH B:410BINDING SITE FOR RESIDUE 1YA B 301
6AC6SOFTWARELYS B:9 , ASN B:35 , GLU B:77 , PHE B:78 , ASP B:79 , VAL B:106 , PHE B:107 , SER B:109 , ARG B:192 , LEU B:197 , PHE B:219 , TYR B:222 , GLN B:223 , 1YA B:301 , HOH B:405 , HOH B:412 , HOH B:417 , HOH B:470 , HOH B:484 , HOH B:507 , HOH B:579BINDING SITE FOR RESIDUE DAU B 302
7AC7SOFTWAREPHE B:203 , ILE B:227 , ASN B:228 , PHE B:247 , HOH B:446 , HOH B:490 , HOH B:681 , HOH B:682 , HOH B:685 , HOH B:755BINDING SITE FOR RESIDUE MPO B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LY0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:100 -Pro A:101
2Leu B:100 -Pro B:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LY0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LY0)

(-) Exons   (0, 0)

(no "Exon" information available for 4LY0)

(-) 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:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhhh.hhh.eeeee............hhhhhhhhh..ee.hhhhhh.....eeeee......hhhhh....eeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............eehhhhh..........hhhhhhhhhhh.........ee..eeeeeeeeeeee.....eee...eeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ly0 A   0 HMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKLN 270
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269 


Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhhhhhhhhh.hhh.eeeee............hhhhhhhhh..ee.hhhhh......eeeee......hhhhh...eeeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............eehhhhh..........hhhhhhhhhhh.........ee..eeeeeeeeeeee.....eee...eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ly0 B  -1 GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKLNKL 272
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268
   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 4LY0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LY0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LY0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4LY0)

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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4LY0)

(-) Related Entries Specified in the PDB File

4lxq SAME PROTEIN IN COMPLEX WITH DTDP AND 5-N-FORMYL-THF
4lxt SAME PROTEIN IN COMPLEX WITH DTDP-QUI3N AND 5-N-FORMYL-THF
4lxu SAME PROTEIN IN COMPLEX WITH DTDP-FUC3N AND 5-N-FORMYL-THF
4lxx SAME PROTEIN IN COMPLEX WITH DTDP-FUC3NFO AND 5-N-FORMYL-THF
4lxy SAME PROTEIN IN COMPLEX WITH DTDP AND 10-N-FORMYL-THF
4ly3