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(-) Description

Title :  1.7 A CRYSTAL STRUCTURE OF H60C MUTANT OF NITROPHORIN I. HEME COMPLEXED WITH TWO MOLECULES IMIDAZOLE
 
Authors :  S. W. Vetter, D. B. Goodin
Date :  14 Jul 04  (Deposition) - 26 Jul 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lipocalin, Beta Barrel, Heme, Imidazole, Bis-Imidazole Heme, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Vetter, D. B. Goodin
1. 7 A Crystal Structure Of H60C Mutant Of Nitrophorin I. Heme Complexed With Two Molecules Imidazole
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, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD4Ligand/IonIMIDAZOLE
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2IMD2Ligand/IonIMIDAZOLE
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:114 , SER A:116 , SER A:117 , LYS A:149 , HOH A:606 , HOH A:619 , HOH A:638 , HOH A:659 , HOH A:709BINDING SITE FOR RESIDUE PO4 A 601
2AC2SOFTWAREASP B:114 , SER B:116 , SER B:117 , LYS B:149 , HOH B:603 , HOH B:612 , HOH B:626 , HOH B:658 , HOH B:679BINDING SITE FOR RESIDUE PO4 B 602
3AC3SOFTWAREVAL A:26 , TYR A:29 , TYR A:41 , LEU A:45 , LEU A:58 , PHE A:69 , ASP A:71 , PHE A:87 , LYS A:89 , TYR A:106 , ILE A:120 , THR A:122 , LEU A:124 , LYS A:126 , IMD A:401 , IMD A:402 , HOH A:627 , HOH A:734 , HOH A:758BINDING SITE FOR RESIDUE HEM A 201
4AC4SOFTWAREVAL B:26 , TYR B:41 , LEU B:58 , PHE B:69 , ASP B:71 , PHE B:87 , LYS B:89 , TYR B:106 , ILE B:120 , LEU B:124 , LYS B:126 , LEU B:131 , IMD B:501 , IMD B:502 , HOH B:660 , HOH B:737BINDING SITE FOR RESIDUE HEM B 202
5AC5SOFTWARELEU A:134 , HEM A:201 , HOH A:651BINDING SITE FOR RESIDUE IMD A 401
6AC6SOFTWARETYR A:59 , CYS A:60 , PHE A:69 , HEM A:201 , HOH A:610BINDING SITE FOR RESIDUE IMD A 402
7AC7SOFTWAREHEM B:202BINDING SITE FOR RESIDUE IMD B 501
8AC8SOFTWARETYR B:59 , CYS B:60 , PHE B:69 , HEM B:202 , HOH B:609BINDING SITE FOR RESIDUE IMD B 502

(-) 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 1U17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U17)

(-) Exons   (0, 0)

(no "Exon" information available for 1U17)

(-) 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:185
 aligned with NP1_RHOPR | Q26239 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:185
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
            NP1_RHOPR    23 GKCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 207
               SCOP domains -d1u17a1 A:2-185 Nitrophorin 1                                                                                                                                                            SCOP domains
               CATH domains 1u17A00 A:1-185  [code=2.40.128.20, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh...eeeeeeeee..........eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeeeeeee.....eee......eeeeeeeee...eeeeeeeee....eeeeeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u17 A   1 MKCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYCYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180     


Chain B from PDB  Type:PROTEIN  Length:185
 aligned with NP1_RHOPR | Q26239 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:185
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
            NP1_RHOPR    23 GKCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYHYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 207
               SCOP domains d1u17b_ B: Nitrophorin 1                                                                                                                                                                  SCOP domains
               CATH domains 1u17B00 B:1-185  [code=2.40.128.20, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhh...eeeeeeeee..........eeeeeeeee..eeeeeeeee......eeeeeeeeeeee..eeeeeeeee.....eee.....eeeeeeeeee...eeeeeeeeee...eeeeeeeeee.......hhhhhhhhhhh..hhhhhee........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u17 B   1 MKCTKNALAQTGFNKDKYFNGDVWYVTDYLDLEPDDVPKRYCAALAAGTASGKLKEALYCYDPKTQDTFYDVSELQEESPGKYTANFKKVEKNGNVKVDVTSGNYYTFTVMYADDSSALIHTCLHKGNKDLGDLYAVLNRNKDTNAGDKVKGAVTAASLKFSDFISTKDNKCEYDNVSLKSLLTK 185
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (0, 0)

(no "Pfam Domain" information available for 1U17)

(-) 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 1u18 2np1 3np1 4np1

(-) Related Entries Specified in the PDB File

1u18