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(-) Description

Title :  CRYSTAL STRUCTURE OF THE E.COLI DHAR(N)-DHAK(T79L) COMPLEX
 
Authors :  R. Shi, L. Mcdonald, M. Cygler, I. Ekiel
Date :  21 Jul 13  (Deposition) - 29 Jan 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.83
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Coiled-Coil, Helix Rotation, Gaf, Pas, Transcriptional Regulation Complex, Transferase-Transcription Regulator Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Shi, L. Mcdonald, M. Cygler, I. Ekiel
Coiled-Coil Helix Rotation Selects Repressing Or Activating State Of Transcriptional Regulator Dhar.
Structure V. 22 478 2014
PubMed-ID: 24440518  |  Reference-DOI: 10.1016/J.STR.2013.11.012

(-) Compounds

Molecule 1 - PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- BINDING SUBUNIT DHAK
    Chains: A, B
    EC Number: 2.7.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B1200, DHAK, DHAR, JW5187, YCGT
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12
 
Molecule 2 - PTS-DEPENDENT DIHYDROXYACETONE KINASE OPERON REGULATORY PROTEIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B1201, DHAK, DHAR, JW5188, YCGU
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K-12

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:52 , GLY A:53 , HIS A:56 , SER A:80 , LYS A:104 , ASP A:109 , HIS A:218BINDING SITE FOR RESIDUE GOL A 401
2AC2SOFTWAREGLY B:52 , GLY B:53 , HIS B:56 , SER B:80 , LYS B:104 , TYR B:106 , ASP B:109 , HIS B:218BINDING SITE FOR RESIDUE GOL B 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Asp A:31 -Pro A:32
2Ala A:40 -Pro A:41
3Glu A:57 -Pro A:58
4Met A:59 -His A:60
5Asp B:31 -Pro B:32
6Ala B:40 -Pro B:41
7Glu B:57 -Pro B:58
8Met B:59 -His B:60
9Ala C:69 -Pro C:70
10Ala D:69 -Pro D:70

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LRY)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4lrya_ A: automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh....eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee.................eeeeee........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeeee........eeeeeeeeeehhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lry A   1 MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFLSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      


Chain B from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4lryb_ B: automated matches                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhh..eeee....eeee.........eeeeeeee.....hhhhh......eeeeeee....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh....eeeeee..................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.eeeeeeeee...hhhhh.........eeee..........eeee..hhhhhhhhhhhhhhhh..eeeeeeeee....eeeeeeeee.......eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee........eeeeeeeee.hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lry B   1 MKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFLSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK 356
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350      


Chain C from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeeehhhhhhhhhh.........hhhhhh.hhhhhhhhhh..eeee.hhh.hhhhh.eeeeeeeee.....eeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.....eeeehhhhhhhhh.hhhhhh..hhhhhh..hhhhhhhhhhh..eeeeeeeeee..eeeeeeeeeeeee....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lry C  13 SPLIATSWERCNKLMKRETWNVPHQAQGVTFASIYRRKKAMLTLGQAALEDAWEYMAPRECALFILDETACILSRNGDPQTLQQLSALGFNDGTYCAEGIIGTCALSLAAISGQAVKTMADQHFKQVLWNWAFCATPLFDSKGRLTGTIALACPVEQTTAADLPLTLAIAREVGNLLLTDSLLAETNRHLNQLNALLESMDDGVISWDEQGNLQFINAQAARVLRLDATASQGRAITELLTLPAVLQQAIKQAHPLKHVEATFESQHQFIDAVITLKPIIETQGTSFILLLHPV 306
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    


Chain D from PDB  Type:PROTEIN  Length:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....eeeeeehhhhhhhhhhh........hhhhhh.hhhhhhhhhh..eeee.hhh.hhhhh.eeeeeeeee.....eeeeeeeeee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeehhhhhhhh..hhhhhh..hhhhhh..hhhhhhhhhhh..eeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lry D  13 SPLIATSWERCNKLMKRETWNVPHQAQGVTFASIYRRKKAMLTLGQAALEDAWEYMAPRECALFILDETACILSRNGDPQTLQQLSALGFNDGTYCAEGIIGTCALSLAAISGQAVKTMADQHFKQVLWNWAFCATPLFDSKGRLTGTIALACPVEQTTAADLPLTLAIAREVGNLLLTDSLLAETNRHLNQLNALLESMDDGVISWDEQGNLQFINAQAARVLRLDATASQGRAITELLTLPAVLQQAIKQAHPLKHVEATFESQHQFIDAVITLKPIIETQGTSFILLLHPV 306
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  4lry
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Access by UniProt ID/Accession number
  DHAK_ECOLI | P76015
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  DHAR_ECOLI | P76016
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  2.7.-.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
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  DHAK_ECOLI | P76015
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 Related Entries

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

UniProtKB/Swiss-Prot
        DHAK_ECOLI | P76015: 1oi2 1oi3 1uod 1uoe 3pnk 3pnl 3pnm 3pno 3pnq 4lrx
        DHAR_ECOLI | P76016: 4lrx 4lrz

(-) Related Entries Specified in the PDB File

4lrx DHAR(N)-DHAK COMPLEX
4lrz