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(-) Description

Title :  STRUCTURE OF MIXED PII-ADP COMPLEXES FROM S. ELONGATUS
 
Authors :  K. Zeth, K. Forchhammer
Date :  25 Aug 13  (Deposition) - 12 Feb 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Zeth, O. Fokina, K. Forchhammer
Structural Basis And Target-Specific Modulation Of Adp Sensing By The Synechococcus Elongatus Pii Signaling Protein.
J. Biol. Chem. V. 289 8960 2014
PubMed-ID: 24519945  |  Reference-DOI: 10.1074/JBC.M113.536557

(-) Compounds

Molecule 1 - NITROGEN REGULATORY PROTEIN P-II
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET28
    Expression System Vector TypePLASMID
    Organism ScientificSYNECHOCOCCUS ELONGATUS
    Organism Taxid32046
    SynonymPII SIGNAL TRANSDUCING PROTEIN, PII

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)   DEF
Biological Unit 2 (1x)ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:27 , MET A:28 , THR A:29 , GLU A:62 , VAL A:64 , ARG A:101 , ARG A:103 , ILE C:7 , GLY C:35 , PHE C:36 , GLY C:37 , ARG C:38 , GLN C:39 , LYS C:58 , ILE C:86 , GLY C:87 , ASP C:88 , GLY C:89 , LYS C:90 , PHE C:92BINDING SITE FOR RESIDUE ADP C1109
2AC2SOFTWAREILE D:7 , GLY D:35 , PHE D:36 , GLY D:37 , ARG D:38 , LYS D:58 , ILE D:86 , GLY D:87 , GLY D:89 , LYS D:90 , PHE D:92 , GLY E:27 , MET E:28 , THR E:29 , GLU E:62 , VAL E:64 , ARG E:101 , ARG E:103BINDING SITE FOR RESIDUE ADP D1116
3AC3SOFTWAREILE E:7 , GLY E:35 , PHE E:36 , GLY E:37 , ARG E:38 , LYS E:58 , ILE E:86 , GLY E:87 , LYS E:90 , PHE E:92 , GLY F:27 , MET F:28 , THR F:29 , GLU F:62 , VAL F:64 , ARG F:101BINDING SITE FOR RESIDUE ADP E1112
4AC4SOFTWAREGLY D:27 , MET D:28 , THR D:29 , GLU D:62 , VAL D:64 , ARG D:101 , ARG D:103 , ILE F:7 , GLY F:35 , PHE F:36 , GLY F:37 , ARG F:38 , LYS F:58 , ILE F:86 , GLY F:87 , ASP F:88 , GLY F:89 , LYS F:90BINDING SITE FOR RESIDUE ADP F1115
5AC5SOFTWAREILE A:86 , GLY A:87 , LYS A:90 , ARG B:101 , ARG B:103BINDING SITE FOR RESIDUE PO4 B1109

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C3K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe E:36 -Gly E:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C3K)

(-) PROSITE Motifs  (3, 14)

Asymmetric Unit (3, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PII_GLNB_DOMPS51343 P-II protein family profile.GLNB_SYNE71-112
 
 
 
 
 
  6A:1-112
B:1-108
C:1-108
D:1-112
E:1-111
F:1-112
2PII_GLNB_UMPPS00496 P-II protein uridylation site.GLNB_SYNE746-51
 
  2C:50-51
F:51-51
3PII_GLNB_CTERPS00638 P-II protein C-terminal region signature.GLNB_SYNE783-96
 
 
 
 
 
  6A:83-96
B:83-96
C:83-96
D:83-96
E:83-96
F:83-96
Biological Unit 1 (3, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PII_GLNB_DOMPS51343 P-II protein family profile.GLNB_SYNE71-112
 
 
 
 
 
  3-
-
-
D:1-112
E:1-111
F:1-112
2PII_GLNB_UMPPS00496 P-II protein uridylation site.GLNB_SYNE746-51
 
  1-
F:51-51
3PII_GLNB_CTERPS00638 P-II protein C-terminal region signature.GLNB_SYNE783-96
 
 
 
 
 
  3-
-
-
D:83-96
E:83-96
F:83-96
Biological Unit 2 (3, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PII_GLNB_DOMPS51343 P-II protein family profile.GLNB_SYNE71-112
 
 
 
 
 
  3A:1-112
B:1-108
C:1-108
-
-
-
2PII_GLNB_UMPPS00496 P-II protein uridylation site.GLNB_SYNE746-51
 
  1C:50-51
-
3PII_GLNB_CTERPS00638 P-II protein C-terminal region signature.GLNB_SYNE783-96
 
 
 
 
 
  3A:83-96
B:83-96
C:83-96
-
-
-

(-) Exons   (0, 0)

(no "Exon" information available for 4C3K)

(-) 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:98
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:115
                                                                                                                                         112   
                                    10        20        30        40        50        60        70        80        90       100       110 |   
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh...eeeeeeee.-----------------............hhhhhhhhhhhhhhhhh...............eeee......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: A:1-112 UniProt: 1-112                                                                       --- PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4c3k A   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGF-----------------EFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAISAW 115
                                    10        20        30     |   -         -   |    60        70        80        90       100       110     
                                                              36                54                                                             

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh....eeeeeeee------------------...........hhhhhhhhhhhhhhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: B:1-108 UniProt: 1-112                                                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4c3k B   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGF------------------FLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
                                    10        20        30     |   -         -    |   60        70        80        90       100        
                                                              36                 55                                                     

Chain C from PDB  Type:PROTEIN  Length:98
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:108
                                    10        20        30        40        50        60        70        80        90       100        
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhh....eeeeeeeee...----------......eeeeeeeeee...hhhhhhhhhhhhhh......eeeeeee............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: C:1-108 UniProt: 1-112                                                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 4c3k C   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQ----------EYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKN 108
                                    10        20        30        |-        50        60        70        80        90       100        
                                                                 39         50                                                          

Chain D from PDB  Type:PROTEIN  Length:101
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:115
                                                                                                                                         112   
                                    10        20        30        40        50        60        70        80        90       100       110 |   
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhh...eeeeeeeee..--------------.............hhhhhhhhhhhhhhhhh...............eeee......hhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: D:1-112 UniProt: 1-112                                                                       --- PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4c3k D   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGR--------------VEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAISAW 115
                                    10        20        30       | -         -  |     60        70        80        90       100       110     
                                                                38             53                                                              

Chain E from PDB  Type:PROTEIN  Length:96
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:111
                                    10        20        30        40        50        60        70        80        90       100       110 
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADA 111
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh....eeeeeeeee..---------------............hhhhhhhhhhhhhhhhh.........................hhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: E:1-111 UniProt: 1-112                                                                       PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER --------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4c3k E   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGR---------------EFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADA 111
                                    10        20        30       | -         -   |    60        70        80        90       100       110 
                                                                38              54                                                         

Chain F from PDB  Type:PROTEIN  Length:105
 aligned with GLNB_SYNE7 | P0A3F4 from UniProtKB/Swiss-Prot  Length:112

    Alignment length:114
                                                                                                                                         112  
                                    10        20        30        40        50        60        70        80        90       100       110 |  
           GLNB_SYNE7     1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKGQTERYRGSEYTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAI--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhh...eeeeeeeee.....---------.....eeeeeeeeeehhhhhhhhhhhhhhhhh......eeeeeee............hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) PII_GLNB_DOM  PDB: F:1-112 UniProt: 1-112                                                                       -- PROSITE (1)
                PROSITE (2) ---------------------------------------------PII_GL-------------------------------PII_GLNB_CTER ------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 4c3k F   1 MKKIEAIIRPFKLDEVKIALVNAGIVGMTVSEVRGFGRQKG---------YTVEFLQKLKLEIVVEDAQVDTVIDKIVAAARTGEIGDGKIFVSPVDQTIRIRTGEKNADAISA 114
                                    10        20        30        40|        -|       60        70        80        90       100       110    
                                                                   41        51                                                               

   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 4C3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C3K)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (GLNB_SYNE7 | P0A3F4)
molecular function
    GO:0030234    enzyme regulator activity    Binds to and modulates the activity of an enzyme.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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: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:0050790    regulation of catalytic activity    Any process that modulates the activity of an enzyme.
    GO:0006808    regulation of nitrogen utilization    Any process that modulates the frequency, rate or extent of nitrogen utilization.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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        GLNB_SYNE7 | P0A3F41qy7 2jj4 2v5h 2xbp 2xg8 2xul 2xzw 4aff 4c3l 4c3m

(-) Related Entries Specified in the PDB File

4c3l STRUCTURE OF WILDTYPE PII FROM S. ELONGATUS AT HIGH RESOLUTION
4c3m STRUCTURE OF WILDTYPE PII FROM S. ELONGATUS AT MEDIUM RESOLUTION