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(-) Description

Title :  CRYSTAL STRUCTURE WLARD, A SUGAR 3N-FORMYL TRANSFERASE IN THE PRESENCE OF DTDP-FUC3NFO AND 5-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 :  1.45
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fmt, 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  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3FNF2Ligand/Ion(2R,3R,4S,5R,6R)-4-(FORMYLAMINO)-3,5-DIHYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL [(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE(NON-PREFERRED NAME)
4FON2Ligand/IonN-{[4-({[(6R)-2-AMINO-5-FORMYL-4-OXO-1,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)PHENYL]CARBONYL}-L-GLUTAMIC ACID
5MPO4Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:75 , PHE A:78 , GLN A:80 , ILE A:81 , ILE A:82 , ASN A:94 , HIS A:125 , ILE A:127 , ASP A:128 , ASN A:129 , GLY A:130 , ASP A:132 , SER A:191 , ARG A:192 , FNF A:304 , HOH A:403 , HOH A:439 , HOH A:456 , HOH A:820 , EDO B:305BINDING SITE FOR RESIDUE FON A 301
02AC2SOFTWAREPHE A:203 , ILE A:227 , ASN A:228 , PHE A:247 , HOH A:489 , HOH A:528 , HOH A:576BINDING SITE FOR RESIDUE MPO A 302
03AC3SOFTWAREILE A:84 , ASP A:128 , ASN A:129 , ASN A:135 , HOH A:485 , HOH A:547 , HOH A:722 , PHE B:241 , TYR B:244 , HOH B:493BINDING SITE FOR RESIDUE MPO A 303
04AC4SOFTWARELYS A:9 , GLU A:77 , PHE A:78 , ASN A:94 , HIS A:96 , GLY A:105 , VAL A:106 , PHE A:107 , THR A:108 , SER A:109 , ASP A:132 , TYR A:154 , ARG A:192 , LEU A:197 , PHE A:219 , TYR A:222 , GLN A:223 , FON A:301 , HOH A:418 , HOH A:422 , HOH A:429 , HOH A:467 , HOH A:481 , HOH A:510 , HOH A:569 , HOH A:696 , HOH A:751 , HOH A:753BINDING SITE FOR RESIDUE FNF A 304
05AC5SOFTWAREARG A:126 , ASN A:135 , HOH A:485 , HOH A:624BINDING SITE FOR RESIDUE CL A 305
06AC6SOFTWARESER B:75 , PHE B:78 , GLN B:80 , ILE B:81 , ILE B:82 , ASN B:94 , HIS B:125 , ILE B:127 , ASP B:128 , ASN B:129 , GLY B:130 , ASP B:132 , SER B:191 , ARG B:192 , FNF B:304 , HOH B:457 , HOH B:497 , HOH B:498BINDING SITE FOR RESIDUE FON B 301
07AC7SOFTWAREPHE B:203 , ILE B:227 , ASN B:228 , PHE B:247 , HOH B:490 , HOH B:495 , HOH B:544 , HOH B:630BINDING SITE FOR RESIDUE MPO B 302
08AC8SOFTWAREPHE A:241 , TYR A:244 , ASP B:128 , ASN B:129 , ASN B:135 , HOH B:412 , HOH B:518 , HOH B:565 , HOH B:714BINDING SITE FOR RESIDUE MPO B 303
09AC9SOFTWARELYS B:9 , GLU B:77 , PHE B:78 , ASN B:94 , HIS B:96 , GLY B:105 , VAL B:106 , PHE B:107 , THR B:108 , SER B:109 , ASP B:132 , TYR B:154 , ARG B:192 , LEU B:197 , PHE B:219 , TYR B:222 , GLN B:223 , FON B:301 , HOH B:404 , HOH B:426 , HOH B:519 , HOH B:575 , HOH B:576 , HOH B:646 , HOH B:729BINDING SITE FOR RESIDUE FNF B 304
10BC1SOFTWAREILE A:131 , FON A:301 , ASN B:245 , ILE B:259 , HOH B:423BINDING SITE FOR RESIDUE EDO B 305
11BC2SOFTWAREARG B:151 , GLN B:220 , GLU B:221 , HOH B:439 , HOH B:712BINDING SITE FOR RESIDUE EDO B 306
12BC3SOFTWARETRP B:44 , ARG B:151 , LEU B:269 , LYS B:271 , LEU B:272 , HOH B:597BINDING SITE FOR RESIDUE EDO B 307
13BC4SOFTWAREILE A:242 , HOH A:613 , HOH A:674 , PHE B:241 , GLY B:243 , HOH B:493 , HOH B:718BINDING SITE FOR RESIDUE EDO B 308

(-) SS Bonds  (0, 0)

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

(-) 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 4LXX)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LXX)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhhhhhhhhh.hhh.eeeee............hhhhhhhhh..ee.hhhhhh.....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
                 4lxx A  -1 GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKLNK 271
                                     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   


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............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
                 4lxx 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 4LXX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

4lxq SAME PROTEIN IN COMPLEX WITH DTPD AND 5-N-FORMYL-THF
4lxt SAME PROTEIN IN COMPLEX WITH DTPD-QUI3N AND 5-N-FORMYL-THF
4lxu SAME PROTEIN IN COMPLEX WITH DTPD-FUC3N AND 5-N-FORMYL-THF
4lxy
4ly0
4ly3