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(-) Description

Title :  1.4 A CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXIS AT PH=5.6.
 
Authors :  A. Weichsel, J. F. Andersen, S. A. Roberts, W. R. Montfort
Date :  30 Sep 99  (Deposition) - 07 Jul 00  (Release) - 29 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Nitric Oxide Transport, Ferric Heme, Antihistamine, Vasodilator, Lipocalin, , Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Weichsel, J. F. Andersen, S. A. Roberts, W. R. Montfort
Nitric Oxide Binding To Nitrophorin 4 Induces Complete Distal Pocket Burial.
Nat. Struct. Biol. V. 7 551 2000
PubMed-ID: 10876239  |  Reference-DOI: 10.1038/76769

(-) Compounds

Molecule 1 - NITROPHORIN 4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Organ: SALIVARY GLAND
    Expression System Plasmid: PET17B-NP4
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET17B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 22-205
    Organism Scientific: RHODNIUS PROLIXUS
    Organism Taxid: 13249
    Other Details: SALIVARY GLAND

 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
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:25 , TYR A:28 , PRO A:37 , TYR A:40 , LEU A:44 , LEU A:57 , HIS A:59 , PHE A:68 , ASP A:70 , PHE A:86 , LYS A:88 , TYR A:105 , PHE A:107 , LEU A:123 , LYS A:125 , LEU A:133 , HOH A:186 , HOH A:215BINDING SITE FOR RESIDUE HEM A 185

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:35 -Val A:36

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1D3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1D3S)

(-) Exons   (0, 0)

(no "Exon" information available for 1D3S)

(-) 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 d1d3sa_ A: Nitrophorin 4                                                                                                                                                                 SCOP domains
               CATH domains 1d3sA00 A:1-184  [code=2.40.128.20, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhheeeeeeeeeeee..........eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeeeeeee.....eee.....eeeeeeeeee...eeeeeeeeee......eeeeeee.......hhhhhhhhhhh..hhhhhee.hhhh...hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1d3s A   1 ACTKNAIAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQVESLGKYTANFKKVDKNGNVKVAVTAGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDAAAGDKVKSAVSAATLEFSKFISTKENNCAYDNDSLKSLLTK 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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  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: 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 1D3S)

(-) 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 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 3fll 3mvf 3tga 3tgb 3tgc 4gnw 4grj 4hpa 4hpb 4hpc 4hpd 5hwz

(-) Related Entries Specified in the PDB File

1d2u CRYSTAL STRUCTURE OF NITROPHORIN 4, 105 K, PH=7.5
1np4 CRYSTAL STRUCTURE OF NITROPHORIN 4, ROOM TEMPERATURE, PH=5.6