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(-) Description

Title :  CRYSTAL STRUCTURE WLARD, A SUGAR 3N-FORMYL TRANSFERASE IN THE PRESENCE OF DTDP-QUI3N 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 :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Formyltransferase, 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, 16)

Asymmetric/Biological Unit (5, 16)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FON2Ligand/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
4MPO4Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
5T3Q2Ligand/Ion[(3R,4S,5S,6R)-4-AMINO-3,5-DIHYDROXY-6-METHYLOXAN-2-YL][HYDROXY-[[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXOPYRIMIDIN-1-YL)OXOLAN-2-YL]METHOXY]PHOSPHORYL]HYDROGEN PHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:75 , PHE A:78 , GLN A:80 , ILE A:81 , ILE A:82 , ASN A:94 , VAL A:106 , ILE A:127 , ASP A:128 , GLY A:130 , ASP A:132 , SER A:191 , ARG A:192 , T3Q A:305 , HOH A:407 , HOH A:412 , HOH A:426 , HOH A:456 , HOH A:621 , HOH A:762 , HOH A:793 , HOH A:821 , EDO B:304BINDING SITE FOR RESIDUE FON A 301
02AC2SOFTWAREPHE A:203 , ILE A:227 , ASN A:228 , PHE A:247 , HOH A:527 , HOH A:615 , HOH A:651 , HOH A:713BINDING SITE FOR RESIDUE MPO A 302
03AC3SOFTWAREILE A:84 , ASP A:128 , ASN A:129 , ASN A:135 , HOH A:453 , HOH A:610 , HOH A:675 , HOH A:726 , HOH A:806 , PHE B:241 , TYR B:244BINDING SITE FOR RESIDUE MPO A 303
04AC4SOFTWAREPHE A:241 , TYR A:244 , HOH A:544 , HOH A:602 , HOH A:641 , HOH A:728 , HOH A:907 , ILE B:84 , ASP B:128 , ASN B:129 , ASN B:135 , HOH B:499BINDING SITE FOR RESIDUE MPO A 304
05AC5SOFTWARELYS A:9 , GLU A:77 , PHE A:78 , GLY A:105 , VAL A:106 , PHE A:107 , THR A:108 , SER A:109 , TYR A:154 , LEU A:197 , PHE A:219 , TYR A:222 , GLN A:223 , FON A:301 , HOH A:406 , HOH A:422 , HOH A:424 , HOH A:428 , HOH A:433 , HOH A:465 , HOH A:472 , HOH A:487 , HOH A:502 , HOH A:503 , HOH A:599BINDING SITE FOR RESIDUE T3Q A 305
06AC6SOFTWARELYS A:204 , ASN A:245 , ILE A:259 , HOH A:451 , FON B:301BINDING SITE FOR RESIDUE EDO A 306
07AC7SOFTWAREASN A:37 , ASP A:38 , LYS A:39 , ILE A:41 , GLN A:45 , HOH A:535 , HOH A:608 , HOH A:626 , HOH A:687BINDING SITE FOR RESIDUE EDO A 307
08AC8SOFTWAREASP A:194 , ASN A:196 , HIS A:199 , HOH A:501 , HOH A:758 , HOH A:765 , HOH A:776BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWARELYS A:9 , ASN A:35 , ASN A:37BINDING SITE FOR RESIDUE CL A 309
10BC1SOFTWAREEDO A:306 , SER B:75 , PHE B:78 , ASP B:79 , GLN B:80 , ILE B:81 , ILE B:82 , ASN B:94 , ILE B:127 , ASP B:128 , GLY B:130 , ASP B:132 , SER B:191 , ARG B:192 , T3Q B:303 , HOH B:419 , HOH B:428 , HOH B:430 , HOH B:436 , HOH B:632 , HOH B:644 , HOH B:664 , HOH B:715BINDING SITE FOR RESIDUE FON B 301
11BC2SOFTWAREPHE B:203 , ILE B:227 , ASN B:228 , PHE B:247 , HOH B:484 , HOH B:516 , HOH B:597 , HOH B:614BINDING SITE FOR RESIDUE MPO B 302
12BC3SOFTWARELYS B:9 , GLU B:77 , PHE B:78 , GLY B:105 , PHE B:107 , THR B:108 , SER B:109 , TYR B:154 , LEU B:197 , PHE B:219 , TYR B:222 , GLN B:223 , FON B:301 , HOH B:404 , HOH B:409 , HOH B:412 , HOH B:448 , HOH B:453 , HOH B:454 , HOH B:479 , HOH B:482 , HOH B:510 , HOH B:520 , HOH B:542 , HOH B:559BINDING SITE FOR RESIDUE T3Q B 303
13BC4SOFTWAREILE A:131 , FON A:301 , LYS B:204 , ASN B:245 , ILE B:259 , HOH B:413BINDING SITE FOR RESIDUE EDO B 304
14BC5SOFTWARETRP B:44 , ARG B:151 , PHE B:155 , LEU B:269 , ASN B:270 , LYS B:271 , LEU B:272 , HOH B:467 , HOH B:550BINDING SITE FOR RESIDUE EDO B 305
15BC6SOFTWARELYS B:9 , ASN B:35 , ASN B:37BINDING SITE FOR RESIDUE CL B 306
16BC7SOFTWAREASN A:115 , ASN A:116 , HOH A:774 , TYR B:103 , SER B:188 , HOH B:445BINDING SITE FOR RESIDUE EDO B 307

(-) SS Bonds  (0, 0)

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

(-) 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 4LXT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LXT)

(-) 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.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
                 4lxt 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....eeeee.......ee....hhhhhh...eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..............eehhhhh..........hhhhhhhhhhh.........ee..eeeeeeeeeeee.....eee...eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxt 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 4LXT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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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
4lxu
4lxx
4lxy
4ly0
4ly3