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(-) Description

Title :  STRUCTURAL BASIS OF A RATIONALLY REWIRED PROTEIN-PROTEIN INTERFACE (HK853WT AND RR468MUTANT V13P, L14I, I17M AND N21V)
 
Authors :  A. I. Podgornaia, P. Casino, A. Marina, M. T. Laub
Date :  19 Feb 13  (Deposition) - 04 Sep 13  (Release) - 25 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Bergerat Fold, Four Helix Bundle, Alpha/Beta Fold, Signal Transduction, Histidine Kinase, Autophosphorylation, Phosphotransferase, Dephosphorylation, Transferase-Signaling Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Podgornaia, P. Casino, A. Marina, M. T. Laub
Structural Basis Of A Rationally Rewired Protein-Protein Interface Critical To Bacterial Signaling
Structure V. 21 1636 2013
PubMed-ID: 23954504  |  Reference-DOI: 10.1016/J.STR.2013.07.005

(-) Compounds

Molecule 1 - HISTIDINE KINASE
    Chains: A, B
    EC Number: 2.7.13.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: K-12
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HK853 CYTOPLASMIC REGION, UNP RESIDUES 232-489
    Gene: TM_0853
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: SENSOR HISTIDINE KINASE
 
Molecule 2 - RESPONSE REGULATOR
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22
    Expression System Strain: K-12
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM_0468
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 243274
    Strain: MSB8
    Synonym: RR468, RESPONSE REGULATOR RECEIVER PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BFD2Mod. Amino AcidASPARTATE BERYLLIUM TRIFLUORIDE
3CL1Ligand/IonCHLORIDE ION
4MG4Ligand/IonMAGNESIUM ION
5SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:239 , ARG A:243 , ARG A:246 , ARG A:423 , TYR A:429BINDING SITE FOR RESIDUE SO4 A 501
02AC2SOFTWAREASN A:379 , LYS A:383 , MG A:503 , ADP A:504 , HOH A:608BINDING SITE FOR RESIDUE SO4 A 502
03AC3SOFTWAREASN A:379 , ASN A:380 , LYS A:383 , SO4 A:502 , ADP A:504 , HOH A:608BINDING SITE FOR RESIDUE MG A 503
04AC4SOFTWAREASN A:380 , LYS A:383 , TYR A:384 , ASP A:411 , ILE A:416 , ILE A:424 , TYR A:429 , ARG A:430 , VAL A:431 , GLY A:441 , THR A:442 , GLY A:443 , GLY A:445 , LEU A:446 , SER A:470 , PHE A:472 , SO4 A:502 , MG A:503 , HOH A:608BINDING SITE FOR RESIDUE ADP A 504
05AC5SOFTWAREHIS A:260 , ARG B:314 , ARG B:317 , SER B:319BINDING SITE FOR RESIDUE SO4 B 501
06AC6SOFTWAREARG A:314 , ARG A:317 , HIS B:260 , LYS B:386 , LYS B:387 , ASP B:388BINDING SITE FOR RESIDUE SO4 B 502
07AC7SOFTWAREASN B:379 , LYS B:383 , PRO B:440 , GLY B:441 , THR B:442 , ADP B:505BINDING SITE FOR RESIDUE SO4 B 503
08AC8SOFTWAREASN B:380 , LYS B:383 , ADP B:505BINDING SITE FOR RESIDUE MG B 504
09AC9SOFTWAREASN B:380 , LYS B:383 , TYR B:384 , ASP B:411 , ILE B:414 , ILE B:416 , ILE B:424 , TYR B:429 , ARG B:430 , VAL B:431 , GLY B:441 , GLY B:443 , GLY B:445 , LEU B:446 , SER B:470 , PHE B:472 , SO4 B:503 , MG B:504BINDING SITE FOR RESIDUE ADP B 505
10BC1SOFTWAREARG B:314BINDING SITE FOR RESIDUE CL B 506
11BC2SOFTWAREASP C:10 , BFD C:53 , MET C:55 , HOH C:304BINDING SITE FOR RESIDUE MG C 201
12BC3SOFTWAREASP D:10 , BFD D:53 , MET D:55BINDING SITE FOR RESIDUE MG D 201

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:330 -A:359
2B:330 -B:359

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Cys A:359 -Pro A:360
2Lys C:105 -Pro C:106
3Lys D:105 -Pro D:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JAV)

(-) 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:246
                                                                                                                                                                                                                                                                                      
               SCOP domains d4java1 A:234-320 automated matches                                                    d4java2 A:321-479 automated matches                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeehhhhhhhhhhhhhhhhhh..eeeeeee......eeeehhhhhhhhhhhhhhhhhhh.......eeeeeeeee...eeeeeeee.....hhhhhhhhhh.................hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jav A 234 NVTESKELERLKRIDRMKTEFIANISHELRTPLTAIKAYAETIYNSLGELDLSTLKEFLEVIIDQSNHLENLLNELLDFSRLERKSLQINREKVDLCDLVESAVNAIKEFASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDEKDGGVLIIVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGKGSRFFVWIPKD 479
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      


Chain B from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains d4javb1 B:236-320 automated matches                                                  d4javb2 B:321-479 automated matches                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh..eeeeeee......eeeehhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeee.....hhhhhhhhhh.................hhhhhhhhhhhhh..eeeeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jav B 236 TESKELERLKRIDRMKTEFIANISHELRTPLTAIKAYAETIYNSLGELDLSTLKEFLEVIIDQSNHLENLLNELLDFSRLERKSLQINREKVDLCDLVESAVNAIKEFASSHNVNVLFESNVPCPVEAYIDPTRIRQVLLNLLNNGVKYSKKDAPDKYVKVILDEKDGGVLIIVEDNGIGIPDHAKDRIFEQFYRVDSSLTYEVPGTGLGLAITKEIVELHGGRIWVESEVGKGSRFFVWIPKD 479
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475    


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains d4javc_ C: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhhh.hhhhh.eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jav C   2 SKKVLLVDDSAPIRKMVSFVLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLNE 122
                                    11        21        31        41        51 |      61        71        81        91       101       111       121 
                                                                              53-BFD                                                                 


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains d4javd_ D: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhhh.eeeee.hhhhhhhhhh.....eeee.......hhhhhhhhhhhh.hhhhh.eeeee....hhhhhhhhhh...eeee...hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4jav D   2 SKKVLLVDDSAPIRKMVSFVLKKEGYEVIEAENGQIALEKLSEFTPDLIVLdIMMPVMDGFTVLKKLQEKEEWKRIPVIVLTAKGGEEDESLALSLGARKVMRKPFSPSQFIEEVKHLLN 121
                                    11        21        31        41        51 |      61        71        81        91       101       111       121
                                                                              53-BFD
   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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q9WYT9_THEMA | Q9WYT9: 3dge 3dgf 3gl9 4ja2 4jas
        Q9WZV7_THEMA | Q9WZV7: 2c2a 3dge 4jas 4jau 4kp4

(-) Related Entries Specified in the PDB File

4ja2 4jas 4jau