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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TANDEM GAF DOMAINS FROM A CYANOBACTERIAL ADENYLYL CYCLASE: NOVEL MODES OF LIGAND-BINDING AND DIMERIZATION
 
Authors :  S. E. Martinez, S. Bruder, A. Schultz, N. Zheng, J. E. Schultz, J. A. Beav J. U. Linder
Date :  17 Jan 05  (Deposition) - 22 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gaf Domain, Bound Cyclic Amp Ligand, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. E. Martinez, S. Bruder, A. Schultz, N. Zheng, J. E. Schultz, J. A. Beavo, J. U. Linder
Crystal Structure Of The Tandem Gaf Domains From A Cyanobacterial Adenylyl Cyclase: Modes Of Ligand Binding An Dimerization
Proc. Natl. Acad. Sci. Usa V. 102 3082 2005
PubMed-ID: 15708973  |  Reference-DOI: 10.1073/PNAS.0409913102

(-) Compounds

Molecule 1 - ADENYLATE CYCLASE
    Chains: A, B
    EC Number: 4.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: CLONED INTO QIAGEN PLASMID PQE-60 AT THE NCOI-BAMH1 SITES
    Expression System Strain: E. COLI BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYAB2
    Organism Scientific: ANABAENA SP.
    Organism Taxid: 1167

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CMP4Ligand/IonADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:103 , THR A:105 , ALA A:122 , ILE A:131 , GLY A:138 , ILE A:139 , ALA A:140 , PHE A:164 , THR A:176 , MET A:179 , GLN A:196 , LEU A:198 , HOH A:517 , HOH A:536 , HOH A:599BINDING SITE FOR RESIDUE CMP A 501
2AC2SOFTWAREARG A:291 , THR A:293 , ILE A:308 , GLY A:325 , PHE A:326 , ALA A:327 , THR A:351 , ALA A:352 , ILE A:355 , THR A:363 , GLN A:383 , VAL A:385 , HOH A:504 , HOH A:507 , HOH A:595 , HOH A:676BINDING SITE FOR RESIDUE CMP A 502
3AC3SOFTWAREARG B:103 , THR B:105 , ILE B:131 , GLY B:138 , ILE B:139 , ALA B:140 , PHE B:164 , THR B:176 , MET B:179 , GLN B:196 , LEU B:198 , HOH B:514 , HOH B:516 , HOH B:687BINDING SITE FOR RESIDUE CMP B 503
4AC4SOFTWAREARG B:291 , THR B:293 , ILE B:308 , GLY B:325 , PHE B:326 , ALA B:327 , THR B:351 , ALA B:352 , ASP B:356 , THR B:363 , GLN B:383 , HOH B:507 , HOH B:525 , HOH B:589BINDING SITE FOR RESIDUE CMP B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YKD)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Phe A:154 -Asp A:155
2Phe A:341 -Asp A:342
3Trp A:401 -Pro A:402
4Phe B:154 -Asp B:155
5Phe B:341 -Asp B:342
6Trp B:401 -Pro B:402

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YKD)

(-) 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:383
 aligned with P94182_9NOST | P94182 from UniProtKB/TrEMBL  Length:860

    Alignment length:383
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
         P94182_9NOST    58 VTEVEQKLQIVHQTLSMLDSHGFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSIVAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFYHDPRSIFAQKQEKITGYRTYTMLALPLLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADEQLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDEAKELMNADRSTLWLIDRDRHELWTKITQDNGSTKELRVPIGKGFAGIVAASGQKLNIPFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVALQNAQLFATV 440
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1ykdA01 A:58-251  [code=3.30.450.40, no name defined]                                                                                                                                             1ykdA02 A:252-440  [code=3.30.450.40, no name defined]                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeeeeeeeee....eeeeeee.hhhhh....eee..hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee.........hhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.eeeeeeeeee....eeeeeee.....eeeeeee..hhhhhhhhhhh..eee..hhhhh..hhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee.........hhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ykd A  58 VTEVEQKLQIVHQTLSMLDSHGFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSIVAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFYHDPRSIFAQKQEKITGYRTYTMLALPLLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADEQLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDEAKELMNADRSTLWLIDRDRHELWTKITQDNGSTKELRVPIGKGFAGIVAASGQKLNIPFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVALQNAQLFATV 440
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   


Chain B from PDB  Type:PROTEIN  Length:380
 aligned with P94182_9NOST | P94182 from UniProtKB/TrEMBL  Length:860

    Alignment length:384
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
         P94182_9NOST    58 VTEVEQKLQIVHQTLSMLDSHGFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSIVAAGEGDRSLEIRIPADKGIAGEVATFKQVVNIPFDFYHDPRSIFAQKQEKITGYRTYTMLALPLLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADEQLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDEAKELMNADRSTLWLIDRDRHELWTKITQDNGSTKELRVPIGKGFAGIVAASGQKLNIPFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVALQNAQLFATVK 441
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 1ykdB01 B:58-254  [code=3.30.450.40, no name defined]                                                                                                                                                1ykdB02 B:255-441  [code=3.30.450.40, no name defined]                                                                                                                                      CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1ykdB01 B:271-431                                                                                                                                            ---------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1ykdB02 B:271-431                                                                                                                                            ---------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1ykdB03 B:271-431                                                                                                                                            ---------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAF-1ykdB04 B:271-431                                                                                                                                            ---------- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhheeeeeeeeee....eeeeeeee.----....eee..hhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee.........hhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeeeeee....eeeeeee.....eeeeeee..hhhhhhhhhhh..eee..hhhhh..hhhhhhhhhhhh.....eeeeeee.....eeeeeeeeee.........hhhhh...hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ykd B  58 VTEVEQKLQIVHQTLSMLDSHGFENILQEMLQSITLKTGELLGADRTTIFLLDEEKQELWSIVAAG----SLEIRIPADKGIAGEVATFKQVVNIPFDFYHDPRSIFAQKQEKITGYRTYTMLALPLLSEQGRLVAVVQLLNKLKPYSPPDALLAERIDNQGFTSADEQLFQEFAPSIRLILESSRSFYIATQKQRAAAAMMKAVKSLSQSSLDLEDTLKRVMDEAKELMNADRSTLWLIDRDRHELWTKITQDNGSTKELRVPIGKGFAGIVAASGQKLNIPFDLYDHPDSATAKQIDQQNGYRTCSLLCMPVFNGDQELIGVTQLVNKKKTGEFPPYNPETWPIAPECFQASFDRNDEEFMEAFNIQAGVALQNAQLFATVK 441
                                    67        77        87        97       107       117     |   -|      137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437    
                                                                                           123  128
   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  (0, 0)

(no "SCOP Domain" information available for 1YKD)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: GAF (44)
(-)
Family: GAF (30)
(-)
Anabaena sp (1)
1aGAF-1ykdB01B:271-431
1bGAF-1ykdB02B:271-431
1cGAF-1ykdB03B:271-431
1dGAF-1ykdB04B:271-431

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (P94182_9NOST | P94182)
molecular function
    GO:0004016    adenylate cyclase activity    Catalysis of the reaction: ATP = 3',5'-cyclic AMP + diphosphate.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016849    phosphorus-oxygen lyase activity    Catalysis of the cleavage of a phosphorus-oxygen bond by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond.
biological process
    GO:0006171    cAMP biosynthetic process    The chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0009190    cyclic nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a cyclic nucleotide, a nucleotide in which the phosphate group is in diester linkage to two positions on the sugar residue.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  1ykd
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