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(-) Description

Title :  CRYSTAL STRUCTURE OF NADC DELETION MUTANT IN C2221 SPACE GROUP
 
Authors :  W. T. Booth, M. Chruszcz
Date :  27 Jan 16  (Deposition) - 25 Jan 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,E,F,H
Biol. Unit 1:  A,C,E  (2x)
Biol. Unit 2:  B,F,H  (2x)
Keywords :  Quinolinate Phosphoribosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. T. Booth, T. L. Morris, D. P. Mysona, M. J. Shah, L. K. Taylor, T. W. Karlin, K. Clary, K. A. Majorek, L. R. Offermann, M. Chruszcz
Streptococcus Pyogenes Quinolinate-Salvage Pathway - Structural And Functional Studies Of Quinolinate Phosphoribosyl Transferase And Nh3 -Dependent Nad(+) Synthetase.
Febs J. 2017
PubMed-ID: 28618168  |  Reference-DOI: 10.1111/FEBS.14136

(-) Compounds

Molecule 1 - NICOTINATE-NUCLEOTIDE DIPHOSPHORYLASE (CARBOXYLATING)
    Chains: A, B, C, E, F, H
    EC Number: 2.4.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJEXPRESS411
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: NADC, HMPREF1231_0804
    Organism Scientific: STREPTOCOCCUS PYOGENES GA06023
    Organism Taxid: 1115816

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCEFH
Biological Unit 1 (2x): A CE  
Biological Unit 2 (2x):  B  FH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 20)

Asymmetric Unit (1, 20)
No.NameCountTypeFull Name
1SO420Ligand/IonSULFATE ION
Biological Unit 1 (1, 20)
No.NameCountTypeFull Name
1SO420Ligand/IonSULFATE ION
Biological Unit 2 (1, 20)
No.NameCountTypeFull Name
1SO420Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:242 , ARG E:190binding site for residue SO4 A 301
02AC2SOFTWAREARG A:242 , ARG E:190 , PHE E:195binding site for residue SO4 A 302
03AC3SOFTWARELYS A:140 , SER A:267 , GLY A:268 , HIS A:272binding site for residue SO4 A 303
04AC4SOFTWAREARG A:139 , ARG A:162 , MET A:170 , LYS A:172binding site for residue SO4 A 304
05AC5SOFTWAREARG B:139 , ARG B:162 , MET B:170 , LYS B:172binding site for residue SO4 B 301
06AC6SOFTWARELYS B:140 , GLY B:268 , SER B:269 , HIS B:272binding site for residue SO4 B 302
07AC7SOFTWARELYS B:140 , ARG H:105binding site for residue SO4 B 303
08AC8SOFTWARELYS C:49 , SER C:280 , LYS C:282binding site for residue SO4 C 301
09AC9SOFTWARELYS C:140 , GLY C:268binding site for residue SO4 C 302
10AD1SOFTWAREARG E:242binding site for residue SO4 E 301
11AD2SOFTWAREARG C:105 , LYS E:140 , LYS E:172 , GLU E:202 , HOH E:402binding site for residue SO4 E 302
12AD3SOFTWAREARG E:139 , ARG E:162 , MET E:170 , LYS E:172 , HOH E:401 , HOH E:406binding site for residue SO4 E 303
13AD4SOFTWARELYS E:140 , GLY E:268 , HIS E:272binding site for residue SO4 E 304
14AD5SOFTWAREARG F:139 , ARG F:162 , LYS F:172binding site for residue SO4 F 301
15AD6SOFTWARELYS F:140 , SER F:267 , GLY F:268 , SER F:269 , HIS F:272binding site for residue SO4 F 302
16AD7SOFTWAREARG F:62 , SO4 H:303binding site for residue SO4 F 303
17AD8SOFTWAREARG H:139 , ARG H:162 , MET H:170 , LYS H:172binding site for residue SO4 H 301
18AD9SOFTWARELYS H:140 , GLY H:268 , HIS H:272binding site for residue SO4 H 302
19AE1SOFTWARESO4 F:303 , ARG H:62 , THR H:65binding site for residue SO4 H 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HUO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HUO)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huo A   6 TDLTPFQIDDTLKAALREDVHSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAVGSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   


Chain B from PDB  Type:PROTEIN  Length:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huo B   6 TDLTPFQIDDTLKAALREDVHSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAVGSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285   


Chain C from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhh......eeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhh.hhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huo C   6 TDLTPFQIDDTLKAALREDVHSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIASVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 ||    188       198       208       218       228       238       248       258       268       278       288
                                                                                                                                                                                                     177|                                                                                                           
                                                                                                                                                                                                      181                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhhh...eeeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5huo E   6 TDLTPFQIDDTLKAALREDVHSEDYSTNAIFHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAVGSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    15        25        35||      46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286  
                                                         36|                                                                                                                                                                                                                                                          
                                                          38                                                                                                                                                                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh...hhhhhhhh....eeeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huo F   5 STDLTPFQIDDTLKAALREDVHSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAAVGSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284    


Chain H from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...hhhhhhh......eeeeeee...ee..hhhhhhhhhhhhh..eee.........ee....eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee........hhhhhhhhhhhh............eeehhhhhh...hhhhhhhhhhhh.....eeeee.hhhhhhhhhhh...eeeee..hhhhhhhhhhhhh...eeeee......hhhhhh.....eee.hhhhhh.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5huo H   6 TDLTPFQIDDTLKAALREDVHSEDYSTNAIFDHHGQAKVSLFAKEAGVLAGLTVFQRVFTLFDEVTFQNPHQFKDGDRLTSGDLVLEIIGSVRSLLTCERVALNFLQHLSGIASMTAAYVEALGDDRIKVFDTRKTTPNLRLFEKYAVRVGGGYNHRFNLSDAIMLKDNHIAVGSVQKAIAQARAYAPFVKMVEVEVESLAAAEEAAAAGVDIIMLDNMSLEQIEQAITLIAGRSRIECSGNIDMTTISRFRGLAIDYVSSGSLTHSAKSLDFSMKGLTYLD 288
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175 ||    186       196       206       216       226       236       246       256       266       276       286  
                                                                                                                                                                                                     177|                                                                                                             
                                                                                                                                                                                                      179
   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 5HUO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5huh
5huj
5hul 5HUL IS THE STRUCTURE OF THE SAME PROTEIN IN A DIFFERENT SPACE GROUP
5hup