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(-) Description

Title :  CRYSTAL STRUCTURE OF PYROCOCCUS HORIKOSHII QUINOLINATE SYNTHASE (NADA) WITH BOUND DIHYDROXYACETONE PHOSPHATE (DHAP) AND FE4S4 CLUSTER
 
Authors :  M. K. Fenwick, S. E. Ealick
Date :  12 Jul 16  (Deposition) - 27 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym./Biol. Unit :  A
Keywords :  Dehydratase, Iron-Sulfur Cluster, Substrate Complex, Biosynthetic Enzyme, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. K. Fenwick, S. E. Ealick
Crystal Structures Of The Iron-Sulfur Cluster-Dependent Quinolinate Synthase In Complex With Dihydroxyacetone Phosphate, Iminoaspartate Analogues, And Quinolinate.
Biochemistry V. 55 4135 2016
PubMed-ID: 27404889  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00626

(-) Compounds

Molecule 1 - QUINOLINATE SYNTHASE A
    Chains: A
    EC Number: 2.5.1.72
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDESTF1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NADA, PH0013
    Organism Scientific: PYROCOCCUS HORIKOSHII (STRAIN ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
    Organism Taxid: 70601
    Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3NH41Ligand/IonAMMONIUM ION
4SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:83 , MET A:85 , ASN A:111 , CYS A:170 , GLU A:198 , CYS A:256 , 13P A:402binding site for residue SF4 A 401
2AC2SOFTWAREHIS A:21 , TYR A:23 , ASP A:37 , SER A:38 , SER A:126 , HIS A:173 , HIS A:196 , GLU A:198 , SER A:212 , THR A:213 , SF4 A:401 , HOH A:530 , HOH A:542 , HOH A:625binding site for residue 13P A 402
3AC3SOFTWAREILE A:17 , ARG A:44 , ASP A:49 , ALA A:50binding site for residue CL A 403
4AC4SOFTWAREGLN A:244binding site for residue CL A 404
5AC5SOFTWAREASP A:137 , ARG A:239 , TYR A:242 , PRO A:243 , LYS A:245 , PHE A:247binding site for residue NH4 A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:144 -Pro A:145
2Val A:164 -Pro A:165
3Lys A:275 -Tyr A:276

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KTN)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh.eeeeee...hhhhhh...eeehhhhhhhhh......eeeee.hhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhh....eeee...hhhhhh...eee...hhhhhhhhh...eeeee.hhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhh...eeee....hhhhhh...ee.hhhhhhhhhhhh.eeeee..hhhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ktn A  -3 GSFTMDLVEEILRLKEERNAIILAHNYQLPEVQDIADFIGDSLELARRATRVDADVIVFAGVDFMAETAKILNPDKVVLIPSREATCAMANMLKVEHILEAKRKYPNAPVVLYVNSTAEAKAYADVTVTSANAVEVVKKLDSDVVIFGPDKNLAHYVAKMTGKKIIPVPSKGHCYVHQKFTLDDVERAKKLHPNAKLMIHPECIPEVQEKADIIASTGGMIKRACEWDEWVVFTEREMVYRLRKLYPQKKFYPAREDAFCIGMKAITLKNIYESLKDMKYKVEVPEEIARKARKAIERMLEMSK 300
                                     6        16        26        36        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       296
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5KTN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:144 - Pro A:145   [ RasMol ]  
    Lys A:275 - Tyr A:276   [ RasMol ]  
    Val A:164 - Pro A:165   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        NADA_PYRHO | O57767: 1wzu 4zk6 5ktm 5kto 5ktp 5ktr 5kts 5ktt

(-) Related Entries Specified in the PDB File

5ktm 5kto 5ktp 5ktr 5kts 5ktt