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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF THE CORE DOMAIN OF NAFY FROM AZOTOBACTER VINELANDII DETERMINED AT 1.8 RESOLUTION
 
Authors :  D. H. Dyer, L. M. Rubio, J. B. Thoden, H. M. Holden, P. W. Ludden, I. Rayment
Date :  08 May 03  (Deposition) - 19 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribonuclease H Motif, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Dyer, L. M. Rubio, J. B. Thoden, H. M. Holden, P. W. Ludden, I. Rayment
The Three-Dimensional Structure Of The Core Domain Of Nafy From Azotobacter Vinelandii Determined At 1. 8 A Resolution
J. Biol. Chem. V. 278 32150 2003
PubMed-ID: 12754195  |  Reference-DOI: 10.1074/JBC.M304264200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CORE DOMAIN
    Gene: NAFY
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354
    Synonym: NAFY PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:105 , GLN A:132 , ASP A:137 , ALA A:138 , SER A:139BINDING SITE FOR RESIDUE EDO A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P90)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P90)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P90)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P90)

(-) Exons   (0, 0)

(no "Exon" information available for 1P90)

(-) 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:123
 aligned with Q9F5X9_AZOVI | Q9F5X9 from UniProtKB/TrEMBL  Length:243

    Alignment length:123
                                   108       118       128       138       148       158       168       178       188       198       208       218   
         Q9F5X9_AZOVI    99 ERVPEGSIRVAIASNNGEQLDGHFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPAAAKVVRAGIHPLKKPKGCAAQEAIAELQTVMAGSPPPWLAKLV 221
               SCOP domains d1p90a_ A: NafY core domain                                                                                                 SCOP domains
               CATH domains 1p90A00 A:99-221  [code=3.30.420.130, no name defined]                                                                      CATH domains
               Pfam domains ---------------Nitro_FeMo-Co-1p90A01 A:114-207                                                               -------------- Pfam domains
         Sec.struct. author ......eeeeeeee....ee........eeeeeeee...eeeeeeee.hhhhhh.hhhhhhhhhh....eeee...hhhhhhhhhhh..eeee....eehhhhhhhhhhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p90 A  99 ERVPEGSIRVAIASNNGEQLDGHFGSCLRFLVYQVSAKDASLVDIRSTLDVALAEDKNAWRVEQIQDCQVLYVVSIGGPAAAKVVRAGIHPLKKPKGCAAQEAIAELQTVMAGSPPPWLAKLV 221
                                   108       118       128       138       148       158       168       178       188       198       208       218
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Nitro_FeMo-Co] (9)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9F5X9_AZOVI | Q9F5X9)
molecular function
    GO:0051540    metal cluster binding    Interacting selectively and non-covalently with a cluster of atoms including both metal ions and nonmetal atoms, usually sulfur and oxygen. Examples include iron-sulfur clusters and nickel-iron-sulfur clusters.
biological process
    GO:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.
    GO:0009399    nitrogen fixation    The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.

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        Q9F5X9_AZOVI | Q9F5X9: 2kic

(-) Related Entries Specified in the PDB File

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