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(-) Description

Title :  CRYSTAL STRUCTURE OF E55Q MUTANT OF NITROPHORIN 4
 
Authors :  W. R. Montfort, A. Weichsel
Date :  18 Dec 08  (Deposition) - 10 Feb 09  (Release) - 14 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Lipocalin, Heme, Mutant, Ammonia, Iron, Metal- Binding, Secreted, Vasoactive, Vasodilator, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. E. Berry, M. N. Shokhirev, A. Y. Ho, F. Yang, T. K. Shokhireva, H. Zhang, A. Weichsel, W. R. Montfort, F. A. Walker
Effect Of Mutation Of Carboxyl Side-Chain Amino Acids Near The Heme On The Midpoint Potentials And Ligand Binding Constants Of Nitrophorin 2 And Its No, Histamine, And Imidazole Complexes.
J. Am. Chem. Soc. V. 131 2313 2009
PubMed-ID: 19175316  |  Reference-DOI: 10.1021/JA808105D
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITROPHORIN-4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 22-205
    Mutation: YES
    Organism Common: TRIATOMID BUG
    Organism Scientific: RHODNIUS PROLIXUS
    Organism Taxid: 13249
    Synonym: NP4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2NH31Ligand/IonAMMONIA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:25 , TYR A:28 , VAL A:36 , TYR A:40 , LEU A:57 , HIS A:59 , PHE A:68 , ASP A:70 , PHE A:86 , LYS A:88 , TYR A:105 , LEU A:123 , LYS A:125 , LYS A:128 , LEU A:133 , NH3 A:186 , HOH A:217BINDING SITE FOR RESIDUE HEM A 185
2AC2SOFTWAREHEM A:185 , HOH A:240BINDING SITE FOR RESIDUE NH3 A 186

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:2 -A:122
2A:41 -A:171

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FLL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FLL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FLL)

(-) Exons   (0, 0)

(no "Exon" information available for 3FLL)

(-) 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:184
 aligned with NP4_RHOPR | Q94734 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:184
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
            NP4_RHOPR    22 ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK 205
               SCOP domains d3flla_ A: Nitrophorin 4                                                                                                                                                                 SCOP domains
               CATH domains 3fllA00 A:1-184  [code=2.40.128.20, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhheeeeeeeeeeee..........eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeee.eee.....eee......eeeeeeeee...eeeeeeeee.......eeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fll A   1 ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKQALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   Legend:   → Mismatch (orange background)
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  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: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FLL)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NP4_RHOPR | Q94734)
molecular function
    GO:0051381    histamine binding    Interacting selectively and non-covalently with histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0070026    nitric oxide binding    Interacting selectively and non-covalently with nitric oxide (NO).
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0050880    regulation of blood vessel size    Any process that modulates the size of blood vessels.
    GO:0042311    vasodilation    An increase in the internal diameter of blood vessels, especially arterioles or capillaries, due to relaxation of smooth muscle cells that line the vessels, and usually resulting in a decrease in blood pressure.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NP4_RHOPR | Q94734: 1d2u 1d3s 1eqd 1erx 1ike 1ikj 1koi 1ml7 1np4 1sxu 1sxw 1sxx 1sxy 1sy0 1sy1 1sy2 1sy3 1u0x 1x8n 1x8o 1x8p 1x8q 1ywa 1ywb 1ywc 1ywd 2at0 2at3 2at5 2at6 2at8 2ofm 2ofr 3c76 3c77 3c78 3mvf 3tga 3tgb 3tgc 4gnw 4grj 4hpa 4hpb 4hpc 4hpd 5hwz

(-) Related Entries Specified in the PDB File

1d2u THE SAME PROTEIN, WILD-TYPE, AMMONIA COMPLEX