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(-) Description

Title :  CRYSTAL STRUCTURE OF NITROPHORIN 2 L122V/L132V MUTANT COMPLEX WITH IMIDAZOLE
 
Authors :  A. Weichsel, W. R. Montfort
Date :  09 Jun 03  (Deposition) - 22 Jun 04  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym./Biol. Unit :  X
Keywords :  Beta Barrel, Lipocalin, Imidazole, Ferric Heme, Blood Clotting Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Weichsel, W. R. Montfort
Conformational Change And Heme Ruffling In Nitrophorin 2, A Nitric Oxide Carrier From Kissing Bug
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITROPHORIN 2
    Chains: X
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET17B
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: RHODNIUS PROLIXUS
    Organism Taxid: 13249
    Synonym: NP2, PROLIXIN-S

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

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
2IMD1Ligand/IonIMIDAZOLE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE X:27 , TYR X:38 , SER X:40 , GLU X:53 , LEU X:55 , HIS X:57 , ASN X:68 , TYR X:85 , TYR X:104 , LEU X:106 , VAL X:122 , LEU X:129 , IMD X:181 , HOH X:223 , HOH X:291 , HOH X:367 , HOH X:391 , HOH X:416 , HOH X:433BINDING SITE FOR RESIDUE HEM X 180
2AC2SOFTWAREILE X:120 , VAL X:122 , GLY X:130 , VAL X:132 , HEM X:180BINDING SITE FOR RESIDUE IMD X 181

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1X:2 -X:121
2X:39 -X:170

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PM1)

(-) Exons   (0, 0)

(no "Exon" information available for 1PM1)

(-) 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 X from PDB  Type:PROTEIN  Length:180
 aligned with NP2_RHOPR | Q26241 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:184
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198    
            NP2_RHOPR    19 MGVSGDCSTNISPKQGLDKAKYFSGKWYVTHFLDKDPQVTDQYCSSFTPRESDGTVKEALYHYNANKKTSFYNIGEGKLESSGLQYTAKYKTVDKKKAVLKEADEKNSYTLTVLEADDSSALVHICLREGSKDLGDLYTVLTHQKDAEPSAKVKSAVTQAGLQLSQFVGTKDLGCQYDDQFTSL 202
               SCOP domains d    1pm1x_ X: Nitrophorin 2 (prolixin-s)                                                                                                                                                SCOP domains
               CATH domains 1    pm1X00 X:0-179  [code=2.40.128.20, no name defined]                                                                                                                                 CATH domains
               Pfam domains ------Nitrophorin-1pm1X01 X:2-179                                                                                                                                                        Pfam domains
         Sec.struct. author .----............hhhhhh...eeeeeee.........eeeeeeeeee..eeeeeeeeee....eeeeeeeeeee.....eeeeeeeee.....eee.....eeeeeeeeee...eeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhh..hhhhhee.hhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm1 X   0 M----DCSTNISPKQGLDKAKYFSGKWYVTHFLDKDPQVTDQYCSSFTPRESDGTVKEALYHYNANKKTSFYNIGEGKLESSGLQYTAKYKTVDKKKAVLKEADEKNSYTLTVLEADDSSALVHICVREGSKDLGDVYTVLTHQKDAEPSAKVKSAVTQAGLQLSQFVGTKDLGCQYDDQFTSL 179
                            |    |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175    
                            |    1                                                                                                                                                                                  
                            0
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (NP2_RHOPR | Q26241)
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

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

UniProtKB/Swiss-Prot
        NP2_RHOPR | Q26241: 1euo 1pee 1t68 2a3f 2acp 2ah7 2al0 2all 2amm 2asn 2eu7 2gtf 2hys

(-) Related Entries Specified in the PDB File

1euo THE AMMONIA COMPLEX OF THE WILD-TYPE PROTEIN
1ikj THE IMIDAZOLE COMPLEX OF A CLOSELY RELATED PROTEIN
1pee THE IMIDAZOLE COMPLEX OF THE WILD-TYPE PROTEIN