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(-) Description

Title :  CRYSTAL STRUCTURE OF WLARD, A SUGAR 3N-FORMYL TRANSFERASE IN THE PRESENCE OF DTPD-QUI3N, DTDP-QUI3NFO, AND 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 :  1.90
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 FORMYLTRANSFERASE
    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, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
11YF1Ligand/Ion[(2R,3R,4S,5S,6R)-4-FORMAMIDO-6-METHYL-3,5-BIS(OXIDANYL)OXAN-2-YL] [[(2R,3S,5R)-5-[5-METHYL-2,4-BIS(OXIDANYLIDENE)PYRIMIDIN-1-YL]-3-OXIDANYL-OXOLAN-2-YL]METHOXY-OXIDANYL-PHOSPHORYL] HYDROGEN PHOSPHATE
21YJ2Ligand/IonN-[4-({[(6R)-2-AMINO-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID
3MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
4T3Q1Ligand/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  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER 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 , GLY A:130 , ASP A:132 , SER A:191 , ARG A:192 , T3Q A:302 , HOH A:427 , HOH A:434 , HOH A:553BINDING SITE FOR RESIDUE 1YJ A 301
2AC2SOFTWARELYS 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 , 1YJ A:301 , HOH A:411 , HOH A:435 , HOH A:570 , HOH A:571 , HOH A:603 , HOH A:627 , HOH A:652 , HOH A:672 , HOH A:673BINDING SITE FOR RESIDUE T3Q A 302
3AC3SOFTWAREPHE A:203 , ILE A:227 , ASN A:228 , PHE A:247 , HOH A:547BINDING SITE FOR RESIDUE MPO A 303
4AC4SOFTWARESER 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 , GLY B:130 , ASP B:132 , SER B:191 , ARG B:192 , 1YF B:302 , HOH B:420 , HOH B:506 , HOH B:563 , HOH B:564BINDING SITE FOR RESIDUE 1YJ B 301
5AC5SOFTWARELYS 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 , LEU B:197 , PHE B:219 , TYR B:222 , GLN B:223 , 1YJ B:301 , HOH B:405 , HOH B:417 , HOH B:418 , HOH B:458 , HOH B:526 , HOH B:573 , HOH B:574 , HOH B:609 , HOH B:701BINDING SITE FOR RESIDUE 1YF B 302
6AC6SOFTWAREPHE B:203 , ILE B:227 , ASN B:228 , PHE B:247 , HOH B:443 , HOH B:481 , HOH B:537 , HOH B:538 , HOH B:616BINDING SITE FOR RESIDUE MPO B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LY3)

(-) 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 4LY3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LY3)

(-) Exons   (0, 0)

(no "Exon" information available for 4LY3)

(-) 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
                 4ly3 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: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
                 4ly3 B  -1 GHMIKICIAGKNNIAVNSLQFILKNYFEADQIVVIPNKNDKGIDSWQKSLLKFALDNNIKIVTLDEIYNIEQIIFFSLEFDQIIKIENFKSDRLFNIHFSALPKYKGVFTSITPILNNELESGVTLHRIDNGIDTGNIIDQHCFPIDINDTARDLYFNYLKYGESIFKKNIQTIINNSYKDLKQTNINSSYFSRKDINLVHKINFKKTSFEIHNQIRAFIFQEYQLPIINNSKIIKSILANEFIGYNVFEEFENYFIISGIDGFKIIAQKL 269
                                     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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    → 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 4LY3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LY3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LY3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4LY3)

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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 4LY3)

(-) 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
4ly0 SAME PROTEIN IN COMPLEX WITH DTDP-GLC AND 10-N-FORMYL-THF