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(-) Description

Title :  ADENYLATE CYCLASE CLASS IV WITH ACTIVE SITE LIGAND 3AT
 
Authors :  D. T. Gallagher, P. T. Reddy
Date :  14 May 10  (Deposition) - 24 Nov 10  (Release) - 22 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cyth Domain, Antiparallel Barrel, Substrate Analog Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. T. Gallagher, S. K. Kim, H. Robinson, P. T. Reddy
Active-Site Structure Of Class Iv Adenylyl Cyclase And Transphyletic Mechanism.
J. Mol. Biol. V. 405 787 2011
PubMed-ID: 21094652  |  Reference-DOI: 10.1016/J.JMB.2010.11.026

(-) Compounds

Molecule 1 - ADENYLATE CYCLASE 2
    Chains: A, B
    EC Number: 4.6.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CYAB, Y3011, YPO1178, YP_0959
    Mutation: YES
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 632
    Synonym: PUTATIVE ADENYLATE CYCLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
13AT2Ligand/Ion3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
2MN2Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:5 , GLU A:10 , GLU A:12 , LYS A:14 , ARG A:63 , LEU A:72 , LYS A:76 , CYS A:83 , LYS A:111 , ARG A:113 , GLU A:136 , MET A:140 , SER A:172 , TYR A:173 , MN A:182 , HOH A:318BINDING SITE FOR RESIDUE 3AT A 181
2AC2SOFTWAREGLU A:12 , GLU A:136 , 3AT A:181BINDING SITE FOR RESIDUE MN A 182
3AC3SOFTWAREPHE B:5 , GLU B:10 , GLU B:12 , LYS B:14 , ARG B:63 , LEU B:72 , LYS B:76 , CYS B:83 , LYS B:111 , ARG B:113 , GLU B:136 , MET B:140 , SER B:172 , TYR B:173 , MN B:182 , HOH B:316 , HOH B:317 , HOH B:357BINDING SITE FOR RESIDUE 3AT B 181
4AC4SOFTWAREGLU B:12 , GLU B:136 , 3AT B:181BINDING SITE FOR RESIDUE MN B 182

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N0Z)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:66 -Pro A:67
2Gly A:77 -Pro A:78
3Asn B:66 -Pro B:67
4Gly B:77 -Pro B:78

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3N0Z)

(-) 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:175
 aligned with Q7CH76_YERPE | Q7CH76 from UniProtKB/TrEMBL  Length:179

    Alignment length:175
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     
         Q7CH76_YERPE     5 FVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
               SCOP domains d3n0za_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeee.....hhhhh.eeeeeeee....eeeeee......eeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhhhh.hhhhh...hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0z A   5 FVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLAKQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174     


Chain B from PDB  Type:PROTEIN  Length:176
 aligned with Q7CH76_YERPE | Q7CH76 from UniProtKB/TrEMBL  Length:179

    Alignment length:176
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173      
         Q7CH76_YERPE     4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLADQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
               SCOP domains d3n0zb_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----CYTH-3n0zB01 B:8-179                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) ----CYTH-3n0zB02 B:8-179                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhh..eeeeeeeeeeeeeeee....hhhhh.eeeeeeee...eeeeeee......eeeee..hhhhhhhhhhhh.eeeeeeeeeeeeeeee..eeeeeeee...eeeeeeeeee.hhhhhhhhhhhhhhhhhh...hhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n0z B   4 HFVGKYEVELKFRVMDLTTLHEQLVAQKATAFTLNNHEKDIYLDANGQDLAKQQISMVLREMNPSGIRLWIVKGPGAERCEASNIEDVSKVQSMLATLGYHPAFTIEKQRSIYFVGKFHITVDHLTGLGDFAEIAIMTDDATELDKLKAECRDFANTFGLQVDQQEPRSYRQLLGF 179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N0Z)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CYTH (6)
(-)
Family: CYTH (4)
(-)
Yersinia pestis (3)
1aCYTH-3n0zB01B:8-179
1bCYTH-3n0zB02B:8-179

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7CH76_YERPE | Q7CH76)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
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).

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 Related Entries

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

UniProtKB/TrEMBL
        Q7CH76_YERPE | Q7CH76: 2fjt 3n0y 3n10

(-) Related Entries Specified in the PDB File

2fjt UNLIGANDED ENZYME
3n0y ENZYME W APC LIGAND
3n10