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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C139A MUTANT OF NOSTOC H-NOX DOMAIN
 
Authors :  V. Kumar, F. Van Den Akker
Date :  06 Dec 12  (Deposition) - 20 Nov 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (3x),B (3x)
Biol. Unit 2:  A  (3x)
Biol. Unit 3:  B  (3x)
Keywords :  Hnox Domain, Soluble Guanylyl Cyclase, C139A Mutant, Nostoc, Heme Binding, No Binding, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Kumar, F. Martin, M. G. Hahn, M. Schaefer, J. S. Stamler, J. P. Stasch F. Van Den Akker
Insights Into Bay 60-2770 Activation And S-Nitrosylation-Dependent Desensitization Of Soluble Guanylyl Cyclase Via Crystal Structures Of Homologous Nosto H-Nox Domain Complexes.
Biochemistry V. 52 3601 2013
PubMed-ID: 23614626  |  Reference-DOI: 10.1021/BI301657W

(-) Compounds

Molecule 1 - ALR2278 PROTEIN
    Chains: A, B
    EC Number: 4.6.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ROSSETTA 2(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HNOX DOMAIN, UNP RESIDUES 1-182
    Gene: ALR2278
    Mutation: YES
    Organism Scientific: NOSTOC SP.
    Organism Taxid: 103690
    Strain: PC 7120

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A (3x)B (3x)
Biological Unit 2 (3x): A 
Biological Unit 3 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLI2Ligand/IonMALONATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLI3Ligand/IonMALONATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLI3Ligand/IonMALONATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
2MLI3Ligand/IonMALONATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , TYR A:2 , TRP A:74 , THR A:78 , TYR A:83 , PHE A:97 , LEU A:101 , HIS A:105 , LEU A:115 , ARG A:116 , PRO A:118 , TYR A:134 , SER A:136 , ARG A:138 , LEU A:141 , VAL A:145 , LEU A:148 , HOH A:608 , HOH A:636BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREHIS A:16 , HIS A:17 , LYS A:61 , LEU A:66 , ALA A:69 , HOH A:739BINDING SITE FOR RESIDUE MLI A 502
3AC3SOFTWAREMET B:1 , TYR B:2 , TRP B:74 , THR B:78 , TYR B:83 , PHE B:97 , LEU B:101 , HIS B:105 , LEU B:115 , ARG B:116 , PRO B:118 , TYR B:134 , SER B:136 , ARG B:138 , VAL B:145 , LEU B:148 , HOH B:318 , HOH B:354BINDING SITE FOR RESIDUE HEM B 201
4AC4SOFTWAREHIS B:16 , HIS B:17 , LYS B:61 , LEU B:66 , ALA B:69BINDING SITE FOR RESIDUE MLI B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IAM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4IAM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IAM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IAM)

(-) Exons   (0, 0)

(no "Exon" information available for 4IAM)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeeeehhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iam A   1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRAGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYE 182
                                    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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh......eeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhh...eeeeeeehhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iam B   1 MYGLVNKAIQDMISKHHGEDTWEAIKQKAGLEDIDFFVGMEAYSDDVTYHLVGAASEVLGKPAEELLIAFGEYWVTYTSEEGYGELLASAGDSLPEFMENLDNLHARVGLSFPQLRPPAFECQHTSSKSMELHYQSTRAGLAPMVLGLLHGLGKRFQTKVEVTQTAFRETGEDHDIFSIKYE 182
                                    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  (0, 0)

(no "SCOP Domain" information available for 4IAM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IAM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IAM)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q8YUQ7_NOSS1 | Q8YUQ7: 2o09 2o0c 2o0g 3l6j 3tf8 3tf9 3tfa 3tfd 3tfe 3tff 3tfg 4iae 4iah 4jqh

(-) Related Entries Specified in the PDB File

2o09 CRYSTAL STRUCTURE OF THE H-NOX DOMAIN FROM NOSTOC SP. PCC 7120
2o0c CRYSTAL STRUCTURE OF THE H-NOX DOMAIN FROM NOSTOC SP. PCC 7120 COMPLEXED TO NO
2o0g CRYSTAL STRUCTURE OF THE H-NOX DOMAIN FROM NOSTOC SP. PCC 7120 COMPLEXED TO CO
3l6j STRUCTURE OF CINACIGUAT (BAY 58-2667) BOUND TO NOSTOC H-NOX DOMAIN
4iae CRYSTAL STRUCTURE OF BAY 60-2770 BOUND TO NOSTOC H-NOX DOMAIN
4iah CRYSTAL STRUCTURE OF BAY 60-2770 BOUND C139A H-NOX DOMAIN WITH S-NITROSYLATED CONSERVED C122