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(-) Description

Title :  CRYSTAL STRUCTURE OF L. MONOCYTOGENES PHOSPHODIESTERASE PGPH HD DOMAIN IN COMPLEX WITH CYCLIC-DI-AMP
 
Authors :  S. Luo, L. Tong
Date :  12 Jan 15  (Deposition) - 11 Feb 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  A (1x),D (1x)
Keywords :  C-Di-Amp, Listeria Monocytogenes, Phosphodiesterase, Hd Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. N. Huynh, S. Luo, D. Pensinger, J. D. Sauer, L. Tong, J. J. Woodward
An Hd-Domain Phosphodiesterase Mediates Cooperative Hydrolysis Of C-Di-Amp To Affect Bacterial Growth And Virulence.
Proc. Natl. Acad. Sci. Usa V. 112 E747 2015
PubMed-ID: 25583510  |  Reference-DOI: 10.1073/PNAS.1416485112

(-) Compounds

Molecule 1 - LMO1466 PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LMO1466, PGPH
    Organism Scientific: LISTERIA MONOCYTOGENES
    Organism Taxid: 169963
    Strain: ATCC BAA-679 / EGD-E

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  D
Biological Unit 3 (1x): A (1x)D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
12BA2Ligand/Ion(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE
2FE4Ligand/IonFE (III) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12BA1Ligand/Ion(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE
2FE-1Ligand/IonFE (III) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12BA1Ligand/Ion(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE
2FE-1Ligand/IonFE (III) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
12BA1Ligand/Ion(2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6-AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3',2'-J][1,3,7,9,2,8]TETRAOXADIPHOSPHACYCLODODECINE-3,5,10,12-TETROL 5,12-DIOXIDE
2FE-1Ligand/IonFE (III) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:544 , HIS A:580 , HIS A:604 , HIS A:605 , FE A:802 , 2BA A:803 , HOH A:972BINDING SITE FOR RESIDUE FE A 801
2AC2SOFTWAREHIS A:514 , HIS A:543 , ASP A:544 , ASP A:648 , FE A:801 , 2BA A:803 , HOH A:972BINDING SITE FOR RESIDUE FE A 802
3AC3SOFTWAREHIS A:514 , ASP A:544 , LYS A:547 , TYR A:553 , PHE A:554 , VAL A:555 , GLU A:556 , HIS A:565 , ILE A:577 , HIS A:580 , HIS A:605 , LEU A:610 , PHE A:613 , TYR A:631 , ASP A:648 , SER A:649 , ALA A:652 , ALA A:653 , ARG A:676 , FE A:801 , FE A:802 , HOH A:911 , HOH A:913 , HOH A:924 , HOH A:928 , HOH A:959 , HOH A:972 , HOH A:979 , HOH A:1004 , HOH A:1005BINDING SITE FOR RESIDUE 2BA A 803
4AC4SOFTWAREASP D:544 , HIS D:580 , HIS D:604 , HIS D:605 , FE D:802 , 2BA D:803 , HOH D:968BINDING SITE FOR RESIDUE FE D 801
5AC5SOFTWAREHIS D:514 , HIS D:543 , ASP D:544 , ASP D:648 , FE D:801 , 2BA D:803 , HOH D:968BINDING SITE FOR RESIDUE FE D 802
6AC6SOFTWARETHR A:658 , GLU A:659 , HIS D:514 , ASP D:544 , LYS D:547 , TYR D:553 , PHE D:554 , VAL D:555 , GLU D:556 , HIS D:565 , ILE D:577 , HIS D:580 , HIS D:605 , LEU D:610 , PHE D:613 , TYR D:631 , ASP D:648 , SER D:649 , ALA D:652 , ALA D:653 , ARG D:676 , FE D:801 , FE D:802 , HOH D:919 , HOH D:929 , HOH D:930 , HOH D:949 , HOH D:967 , HOH D:968 , HOH D:974 , HOH D:1010BINDING SITE FOR RESIDUE 2BA D 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4S1B)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:633 -Pro A:634
2Gly D:633 -Pro D:634

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4S1B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4S1B)

(-) Exons   (0, 0)

(no "Exon" information available for 4S1B)

(-) 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhh.....hhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1b A 498 HPLLKKILMKAPGTYHHSMMVANLAEACADKIGANSLLVRVGCFYHDIGKTLRPPYFVENQINPHDRLTPEQSRDIILSHTKDGAEILKENHMPQPIIDIALQHHGTTLLKYFYFKAKETNPDVKEADYRYSGPKPQTKEIAIINISDSVEAAVRSSTEPTMAKITEIIDGIIKDRFLDGQFTECDITIQEIKIIRDTLIATLNGIYHQRIQY 713
                                   507       517       527       537       547       557||     570       580       590       600       610       620       630       640       650       660       670       680       690       700       710   
                                                                                      558|                                                                                                                                                       
                                                                                       562                                                                                                                                                       


Chain D from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhh.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4s1b D 494 ANPNHPLLKKILMKAPGTYHHSMMVANLAEACADKIGANSLLVRVGCFYHDIGKTLRPPYFVENQLQGINPHDRLTPEQSRDIILSHTKDGAEILKENHMPQPIIDIALQHHGTTLLKYFYFKAKETNPDVKEADYRYSGPKPQTKEIAIINISDSVEAAVRSSTEPTMAKITEIIDGIIKDRFLDGQFTECDITIQEIKIIRDTLIATLNGIY 707
                                   503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703
   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 4S1B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4S1B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4S1B)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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4s1c