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(-) Description

Title :  1.96 A CRYSTAL STRUCTURE OF H60C MUTANT OF NITROPHORIN COMPLEXED WITH HISTAMINE
 
Authors :  S. W. Vetter, D. B. Goodin
Date :  15 Jul 04  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipocalin, Beta Barrel, Ferric Heme, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Vetter, D. B. Goodin
1. 96 A Crystal Structure Of H60C Mutant Of Nitrophorin Complexed With Histamine
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITROPHORIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: RHODNIUS PROLIXUS
    Organism Taxid: 13249
    Synonym: NP1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2HSM2Ligand/IonHISTAMINE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2HSM1Ligand/IonHISTAMINE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2HSM1Ligand/IonHISTAMINE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:114 , SER A:116 , SER A:117 , LYS A:149 , HOH A:424 , HOH A:427 , HOH A:497BINDING SITE FOR RESIDUE PO4 A 301
2AC2SOFTWAREASP B:114 , SER B:116 , SER B:117 , LYS B:149 , HOH B:410 , HOH B:424 , HOH B:438BINDING SITE FOR RESIDUE PO4 B 302
3AC3SOFTWARETYR A:29 , LYS A:39 , TYR A:41 , LEU A:45 , LEU A:58 , ASP A:71 , PHE A:87 , LYS A:89 , TYR A:106 , LEU A:124 , LYS A:126 , HSM A:401 , HOH A:410 , HOH A:454 , HOH A:465 , HOH A:469 , HOH A:520BINDING SITE FOR RESIDUE HEM A 201
4AC4SOFTWARETYR B:29 , LYS B:39 , ASP B:71 , PHE B:87 , LYS B:89 , TYR B:106 , LEU B:124 , LYS B:126 , ALA B:136 , HSM B:402 , HOH B:417 , HOH B:474BINDING SITE FOR RESIDUE HEM B 201
5AC5SOFTWAREASP A:31 , GLU A:33 , LEU A:124 , LEU A:131 , HEM A:201 , HOH A:402 , HOH A:476BINDING SITE FOR RESIDUE HSM A 401
6AC6SOFTWAREASP B:31 , GLU B:33 , LEU B:124 , LEU B:131 , LEU B:134 , HEM B:201 , HOH B:440BINDING SITE FOR RESIDUE HSM B 402

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:3 -A:123
2A:42 -A:172
3B:3 -B:123
4B:42 -B:172

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U18)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U18)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U18)

(-) Exons   (0, 0)

(no "Exon" information available for 1U18)

(-) 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:184
 aligned with NP1_RHOPR | Q26239 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:184
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
            NP1_RHOPR    24 KCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 207
               SCOP domains d1u18a_ A: Nitrophorin 1                                                                                                                                                                 SCOP domains
               CATH domains 1u18A00 A:2-185  [code=2.40.128.20, no name defined]                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhheeeeeeeeeeee..........eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeee..eee.....eee......eeeeeeeee...eeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u18 A   2 KCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYCYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181    


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with NP1_RHOPR | Q26239 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:184
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
            NP1_RHOPR    24 KCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 207
               SCOP domains d1u18b_ B: Nitrophorin 1                                                                                                                                                                 SCOP domains
               CATH domains 1u18B00 B:2-185  [code=2.40.128.20, no name defined]                                                                                                                                     CATH domains
           Pfam domains (1) -Nitrophorin-1u18B01 B:3-182                                                                                                                                                         --- Pfam domains (1)
           Pfam domains (2) -Nitrophorin-1u18B02 B:3-182                                                                                                                                                         --- Pfam domains (2)
         Sec.struct. author ............hhhhhh...eeeeeeeee..........eeeeeeeee..eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeee.....eee......eeeeeeeee...eeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u18 B   2 KCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYCYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 185
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   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  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NP1_RHOPR | Q26239)
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).
biological process
    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

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UniProtKB/Swiss-Prot
        NP1_RHOPR | Q26239: 1np1 1u17 2np1 3np1 4np1

(-) Related Entries Specified in the PDB File

1u17