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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINALLY TAGGED UBID FROM E. COLI RECONSTITUTED WITH PRFMN COFACTOR
 
Authors :  S. A. Marshall, D. Leys
Date :  07 Oct 16  (Deposition) - 11 Jan 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Ubid, Decarboxylase, Ubiquinone Biosynthesis, Prfmn Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Marshall, K. Fisher, A. Ni Cheallaigh, M. D. White, K. A. Payne, D. A. Parker, S. E. Rigby, D. Leys
Oxidative Maturation And Structural Characterization Of Prenylated Fmn Binding By Ubid, A Decarboxylase Involved In Bacterial Ubiquinone Biosynthesis.
J. Biol. Chem. V. 292 4623 2017
PubMed-ID: 28057757  |  Reference-DOI: 10.1074/JBC.M116.762732

(-) Compounds

Molecule 1 - 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE
    Chains: A, B, C
    EC Number: 4.1.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBID, C4790
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: POLYPRENYL P-HYDROXYBENZOATE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
14LU3Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL
2MN3Ligand/IonMANGANESE (II) ION
3NA3Ligand/IonSODIUM ION
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
14LU6Ligand/Ion1-DEOXY-5-O-PHOSPHONO-1-(3,3,4,5-TETRAMETHYL-9,11-DIOXO-2,3,8,9,10,11-HEXAHYDRO-7H-QUINOLINO[1,8-FG]PTERIDIN-12-IUM-7-YL)-D-RIBITOL
2MN-1Ligand/IonMANGANESE (II) ION
3NA-1Ligand/IonSODIUM ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:175 , GLU A:241 , 4LU A:502 , NA A:503binding site for residue MN A 501
02AC2SOFTWARETHR A:160 , ASN A:175 , ILE A:178 , TYR A:179 , ARG A:180 , ARG A:192 , LEU A:194 , ARG A:197 , GLY A:198 , ALA A:231 , VAL A:232 , GLU A:241 , MN A:501 , NA A:503 , HOH A:604binding site for residue 4LU A 502
03AC3SOFTWARELEU A:176 , ALA A:231 , THR A:233 , GLU A:241 , MN A:501 , 4LU A:502 , HOH A:604binding site for residue NA A 503
04AC4SOFTWAREASN B:175 , GLU B:241 , 4LU B:502 , NA B:503 , HOH B:610 , HOH B:615binding site for residue MN B 501
05AC5SOFTWARETHR B:160 , ASN B:175 , LEU B:176 , ILE B:178 , TYR B:179 , ARG B:180 , ARG B:192 , LEU B:194 , ARG B:197 , GLY B:198 , ALA B:231 , VAL B:232 , GLU B:241 , MN B:501 , NA B:503 , HOH B:610 , HOH B:657binding site for residue 4LU B 502
06AC6SOFTWARELEU B:176 , ALA B:231 , GLU B:241 , MN B:501 , 4LU B:502 , HOH B:657binding site for residue NA B 503
07AC7SOFTWARELEU B:389 , ARG B:390 , GLN B:391binding site for residue SO4 B 504
08AC8SOFTWAREASN C:175 , GLU C:241 , 4LU C:502 , NA C:503binding site for residue MN C 501
09AC9SOFTWARETHR C:160 , ASN C:175 , LEU C:176 , ILE C:178 , TYR C:179 , ARG C:180 , ARG C:192 , LEU C:194 , ARG C:197 , GLY C:198 , ALA C:231 , VAL C:232 , GLU C:241 , THR C:320 , MN C:501 , NA C:503binding site for residue 4LU C 502
10AD1SOFTWARELEU C:176 , ALA C:231 , GLU C:241 , MN C:501 , 4LU C:502binding site for residue NA C 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5M1D)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:286 -Pro A:287
2Pro A:325 -Pro A:326
3Gly B:286 -Pro B:287
4Pro B:325 -Pro B:326
5Gly C:286 -Pro C:287
6Pro C:325 -Pro C:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M1D)

(-) Exons   (0, 0)

(no "Exon" information available for 5M1D)

(-) 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:469
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhh......hhhhhhhhhhhhh.hhhhh...eee..hhhhheeee.hhhhhhhh............ee..eeeeee......eeeee..eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh......hhhhhhhhhhh...eeee......eee....eeeeeeeeeeeeeee..ee....eee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhh.hhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee...................hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1d A   6 YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKKQVLNMPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIFN 492
                                    15        25        35        45        55        65        75        85        95||     123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483         
                                                                                                                     96|                                                                                                                                                                                                                                                                                                                                                                                         
                                                                                                                     115                                                                                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhhh...hhhhhhhhhhhhhhh......eee..hhhhheeee.hhhhhhhh............ee..eeeeee......eeeee..eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh......hhhhhhhhhhh...eeee......eee....eeeeeeeeeeeeeee..ee.....ee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee..............ee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1d B   6 YNDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKLNMPTKRLRGAPCQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF 491
                                    15        25        35        45        55        65        75        85        95||     126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486     
                                                                                                                     96|                                                                                                                                                                                                                                                                                                                                                                                     
                                                                                                                     118                                                                                                                                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..eeee.......hhhhhhhhhhhhh...eeee.........eee....hhhhhhhhh...hhhhhhhhhhhhhh.......ee.....ee....hhhhh............ee..eeeeee......eeeee..eeeee..eee......hhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhh......hhhhhhhhhhh...eeee......eee....eeeeeeeeeeeeeee..ee.....ee..eeeeeeeeeeeee.....ee........hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh...eeeeee.....hhhhhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhheeeeeeee............eeeeeeee...................hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m1d C   7 NDLRDFLTLLEQQGELKRITLPVDPHLEITEIADRTLRAGGPALLFENPKGYSMPVLCNLFGTPKRVAMGMGQEDVSALREVGKLLAFLKEPMPTKRLQQKIVSGDDVDLNRIPIMTCWPEDAAPLITWGLTVTRGPHKERQNLGIYRQQLIGKNKLIMRWLSHRGGALDYQEWCAAHPGERFPVSVALGADPATILGAVTPVPDTLSEYAFAGLLRGTKTEVVKCISNDLEVPASAEIVLEGYIEQGETAPEGPYGDHTGYYNEVDSFPVFTVTHITQREDAIYHSTYTGRPPDEPAVLGVALNEVFVPILQKQFPEIVDFYLPPEGCSYRLAVVTIKKQYAGHAKRVMMGVWSFLRQFMYTKFVIVCDDDVNARDWNDVIWAITTRMDPARDTVLVENTPIDYLDFASPVSGLGSKMGLDATNKWPGETQREWGRPIKKDPDVVAHIDAIWDELAIF 491
                                    16        26        36        46        56        66        76        86        96 ||    132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482         
                                                                                                                      98|  125|                                                                                                                                                                                                                                                                                                                                                                        
                                                                                                                      120   131
   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 5M1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M1D)

(-) Gene Ontology  (12, 22)

Asymmetric Unit(hide GO term definitions)

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  5m1d
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  UBID_ECOL6 | P0AAB5
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  UBID_ECOLI | P0AAB4
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  4.1.1.98
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 Related Entries

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

UniProtKB/Swiss-Prot
        UBID_ECOL6 | P0AAB5: 5m1b 5m1c 5m1e
        UBID_ECOLI | P0AAB4: 2idb 5m1b 5m1c 5m1e

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5M1D)