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(-) Description

Title :  CRYSTAL STRUCTURE OF FULL LENGTH RV0805 IN COMPLEX WITH 5'-AMP
 
Authors :  M. Podobnik, U. Dermol
Date :  15 Jul 09  (Deposition) - 29 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metallophosphoesterase, Alpha-Beta Fold, Swapped-Dimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Podobnik, R. Tyagi, N. Matange, U. Dermol, A. K. Gupta, R. Mattoo, K. Seshadri, S. S. Visweswariah
A Mycobacterial Cyclic Amp Phosphodiesterase That Moonlight As A Modifier Of Cell Wall Permeability
J. Biol. Chem. V. 284 32846 2009
PubMed-ID: 19801656  |  Reference-DOI: 10.1074/JBC.M109.049635
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ICC PROTEIN
    Chains: A
    EC Number: 3.1.4.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEXHTC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV0805
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV
    Synonym: RV0805 PHOSPHODIESTERASE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric Unit (6, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2AMP1Ligand/IonADENOSINE MONOPHOSPHATE
3BTB1Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4FE1Ligand/IonFE (III) ION
5MN1Ligand/IonMANGANESE (II) ION
6MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (4, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2AMP2Ligand/IonADENOSINE MONOPHOSPHATE
3BTB2Ligand/Ion2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
4FE-1Ligand/IonFE (III) ION
5MN-1Ligand/IonMANGANESE (II) ION
6MPD6Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:21 , HIS A:23 , ASP A:63 , HIS A:209 , MN A:555 , HOH A:565 , AMP A:666BINDING SITE FOR RESIDUE FE A 444
2AC2SOFTWAREASP A:63 , ASN A:97 , HIS A:169 , HIS A:207 , FE A:444 , HOH A:565 , AMP A:666BINDING SITE FOR RESIDUE MN A 555
3AC3SOFTWAREHIS A:23 , ASP A:63 , ASN A:97 , HIS A:98 , ALA A:157 , MET A:179 , ALA A:180 , THR A:182 , HIS A:207 , LEU A:208 , HIS A:209 , HOH A:359 , FE A:444 , HOH A:474 , HOH A:485 , HOH A:492 , HOH A:495 , HOH A:499 , HOH A:500 , HOH A:549 , MN A:555 , HOH A:565BINDING SITE FOR RESIDUE AMP A 666
4AC4SOFTWAREASP A:66 , LYS A:67 , ASN A:97 , HIS A:98 , ASP A:99 , VAL A:121 , PRO A:137 , GLY A:138 , HIS A:140 , GLU A:155 , HOH A:387 , HOH A:393 , HOH A:512BINDING SITE FOR RESIDUE BTB A 777
5AC5SOFTWAREVAL A:92 , TRP A:93 , ARG A:120 , CYS A:122BINDING SITE FOR RESIDUE MPD A 778
6AC6SOFTWAREASP A:119 , SER A:147 , TRP A:151 , HOH A:383BINDING SITE FOR RESIDUE MPD A 779
7AC7SOFTWAREARG A:77 , GLU A:81 , LEU A:109BINDING SITE FOR RESIDUE MPD A 780
8AC8SOFTWAREALA A:160 , HOH A:481BINDING SITE FOR RESIDUE ACT A 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IB8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3IB8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IB8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IB8)

(-) Exons   (0, 0)

(no "Exon" information available for 3IB8)

(-) 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:295
 aligned with CPDA_MYCTO | P9WP64 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:295
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
           CPDA_MYCTO     4 LRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIPLGGGETVGTFVSPGQARRKIAESGIFIEPSRRD 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......eeeeee..........hhhhh.hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhh.........eeeee..eeeee.............hhhhhhhhhhhh.......eeee.........hhhhhhhh..hhhhhhhhhh...eeeeee......eeeee..eeeee......ee..........ee....eeeeeee....eeeeeee...........hhhhhhhhhhhh.ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ib8 A   4 LRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIPLGGGETVGTFVSPGQARRKIAESGIFIEPSRRD 298
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     


Chain A from PDB  Type:PROTEIN  Length:295
 aligned with CPDA_MYCTU | P9WP65 from UniProtKB/Swiss-Prot  Length:318

    Alignment length:295
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
           CPDA_MYCTU     4 LRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIPLGGGETVGTFVSPGQARRKIAESGIFIEPSRRD 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......eeeeee..........hhhhh.hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhhhhh.eeee......hhhhhhhhhhh.........eeeee..eeeee.............hhhhhhhhhhhh.......eeee.........hhhhhhhh..hhhhhhhhhh...eeeeee......eeeee..eeeee......ee..........ee....eeeeeee....eeeeeee...........hhhhhhhhhhhh.ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ib8 A   4 LRAAEHPRPDYVLLHISDTHLIGGDRRLYGAVDADDRLGELLEQLNQSGLRPDAIVFTGDLADKGEPAAYRKLRGLVEPFAAQLGAELVWVMGNHDDRAELRKFLLDEAPSMAPLDRVCMIDGLRIIVLDTSVPGHHHGEIRASQLGWLAEELATPAPDGTILALHHPPIPSVLDMAVTVELRDQAALGRVLRGTDVRAILAGHLHYSTNATFVGIPVSVASATCYTQDLTVAAGGTRGRDGAQGCNLVHVYPDTVVHSVIPLGGGETVGTFVSPGQARRKIAESGIFIEPSRRD 298
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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 3IB8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IB8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IB8)

(-) Gene Ontology  (20, 29)

Asymmetric Unit(hide GO term definitions)
Chain A   (CPDA_MYCTO | P9WP64)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain A   (CPDA_MYCTU | P9WP65)
molecular function
    GO:0008663    2',3'-cyclic-nucleotide 2'-phosphodiesterase activity    Catalysis of the reaction: nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate.
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    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.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0042301    phosphate ion binding    Interacting selectively and non-covalently with phosphate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0042545    cell wall modification    The series of events leading to chemical and structural alterations of an existing cell wall that can result in loosening, increased extensibility or disassembly.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CPDA_MYCTO | P9WP64: 2hy1 2hyo 2hyp 3ib7
        CPDA_MYCTU | P9WP65: 2hy1 2hyo 2hyp 3ib7

(-) Related Entries Specified in the PDB File

2hy1 CRYSTAL STRUCTURE OF RV0805 CATALYTIC CORE
2hyo CRYSTAL STRUCTURE OF RV0805 CATALYTIC CORE N97A MUTANT
2hyp CRYSTAL STRUCTURE OF RV0805 CATALYTIC CORE D66A MUTANT
3ib7 CRYSTAL STRUCTURE OF FULL LENGTH RV0805