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(-) Description

Title :  CRYSTAL STRUCTURE OF PA01 PROTEIN, PUTATIVE LYSR FAMILY TRANSCRIPTIONAL REGULATOR FROM PSEUDOMONAS AERUGINOSA
 
Authors :  A. A. Knapik, K. L. Tkaczuk, M. Chruszcz, S. Wang, M. D. Zimmerman, M. Cym T. Skarina, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimiak, J. M. W. Minor, Midwest Center For Structural Genomics (Mcsg)
Date :  26 Jan 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lysr, Transcriptional Regulator, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Knapik, K. L. Tkaczuk, M. Chruszcz, S. Wang, M. D. Zimmerman, M. Cymborowski, T. Skarina, O. Kagan, A. Savchenko, A. M. Edwards, A. Joachimiak, J. M. Bujnicki, W. Minor
Crystal Structure Of Pa01 Protein, Putative Lysr Family Transcriptional Regulator From Pseudomonas Aeruginosa
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE TRANSCRIPTIONAL REGULATOR
    Atcc: 15692
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)CODON PLUS RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PA0218
    Organism Scientific: PSEUDOMONAS AERUGINOSA PA01
    Organism Taxid: 208964
    Strain: PA01 / 1C / PRS 101 / LMG 12228

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric/Biological Unit (2, 26)
No.NameCountTypeFull Name
1MSE24Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:138 , GLY B:139 , SER B:142 , ARG B:144 , ARG C:129 , ARG C:144 , HOH C:314BINDING SITE FOR RESIDUE SO4 C 307
2AC2SOFTWAREGLN A:138 , GLY A:139 , SER A:142 , ARG A:144 , ARG D:129 , ARG D:144BINDING SITE FOR RESIDUE SO4 D 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gln A:202 -Pro A:203
2Gln B:202 -Pro B:203
3Gln C:202 -Pro C:203
4Gln D:202 -Pro D:203

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FZV)

(-) 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:285
 aligned with Q9I6S0_PSEAE | Q9I6S0 from UniProtKB/TrEMBL  Length:306

    Alignment length:297
                                    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       
         Q9I6S0_PSEAE     4 YTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLTPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fzvA01 A:4-87 'winged helix'  repressor DN A bi         nding domain               3fzvA02 A:88-164,A:272-300 Periplasmic binding protein-like II               -3fzvA03 A:166-271 Periplasmic binding protein-like II                                                     3fzvA02 A:88-164,A:272-300    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhh...-hhhhhhhhhhhhh-....---------.hhhhhhhhhhhhhhhhhhhhhhhh-........eeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh...eeee........eeeee.......eeeee.........eehhhhhh...eeee...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh....eee..............eeeeee.........eeeee.....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzv A   4 YTLRQLKYFVTTVECGSVAEASRKLYIAQ-SISTAVKGLEESF-VQLF---------LTPAGARFYRKAQELLRmAHEFEQN-LADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLmPPQRPHALLPEGHRFAGQAQVSLRDLCLEPmILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEmVRGmVGQGFGFSLLVTRPHSECTYDGKKVVmVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
                                    13        23        |-|       43  | |  | -       |63        73    |   83 | |    93       103       113       123       133       143       153       163 |     173       183       193  |    203       213       223      |233|      243       253       263       273       283       293       
                                                       32 |          46 | 51        61               78-MSE 85 |                                                                           165-MSE                        196-MSE                           230-MSE                        261-MSE                                   
                                                         34            48                                     87                                                                                                                                                234-MSE                                                              


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with Q9I6S0_PSEAE | Q9I6S0 from UniProtKB/TrEMBL  Length:306

    Alignment length:298
                                    12        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        
         Q9I6S0_PSEAE     3 SYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLTPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fzvB01 B:3-87 'winged helix' repressor DNA bindi        ng domain                   3fzvB02 B:88-164,B:272-300 Periplasmic binding protein-like II               -3fzvB03 B:166-271 Periplasmic binding protein-like II                                                     3fzvB02 B:88-164,B:272-300    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhhh....--------..hhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh...eeee........eeeee.......eeeee.........eehhhhhh...eeee...hhhhhhhhhhhhh.....eeeee.hhhhhhhhhhh....eee..............eeeeee.........eeeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzv B   3 SYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLF--------SLTPAGARFYRKAQELLRmAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLmPPQRPHALLPEGHRFAGQAQVSLRDLCLEPmILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEmVRGmVGQGFGFSLLVTRPHSECTYDGKKVVmVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
                                    12        22        32        42        |-       |62        72     |  82        92       102       112       122       132       142       152       162  |    172       182       192   |   202       212       222       232 |     242       252       262       272       282       292        
                                                                           51       60                78-MSE                                                                                165-MSE                        196-MSE                           230-MSE                        261-MSE                                   
                                                                                                                                                                                                                                                                 234-MSE                                                              


Chain C from PDB  Type:PROTEIN  Length:285
 aligned with Q9I6S0_PSEAE | Q9I6S0 from UniProtKB/TrEMBL  Length:306

    Alignment length:298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291        
         Q9I6S0_PSEAE     2 ASYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLTPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLG 299
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fzvC01 C:2-79 'winged helix' repressor DNA bindin        g domain            3fzvC     02 C:80-164,C:272-299 Periplasmic binding protein-like II                  -3fzvC03 C:166-271 Periplasmic binding protein-like II                                                     3fzvC02 C:80-164,C:272-299   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....--------..hhhhhhhhhhhhhhhhhhhhh..-----.....eeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh...eeee........eeeee.......eeeee.........eehhhhhh..eeeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh....eee..............eeeeee.........eeeee.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzv C   2 ASYTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLF--------SLTPAGARFYRKAQELLRmAHEFEQ-----NDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLmPPQRPHALLPEGHRFAGQAQVSLRDLCLEPmILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEmVRGmVGQGFGFSLLVTRPHSECTYDGKKVVmVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLG 299
                                    11        21        31        41        51        61        71      | 81  |     91       101       111       121       131       141       151       161   |   171       181       191    |  201       211       221       231  |    241       251       261       271       281       291        
                                                                            51       60                78-MSE84    90                                                                        165-MSE                        196-MSE                           230-MSE                        261-MSE                                  
                                                                                                                                                                                                                                                                  234-MSE                                                             


Chain D from PDB  Type:PROTEIN  Length:273
 aligned with Q9I6S0_PSEAE | Q9I6S0 from UniProtKB/TrEMBL  Length:306

    Alignment length:297
                                    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       
         Q9I6S0_PSEAE     4 YTLRQLKYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRHHAQGVSLTPAGARFYRKAQELLRMAHEFEQNALADNDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLMPPQRPHALLPEGHRFAGQAQVSLRDLCLEPMILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEMVRGMVGQGFGFSLLVTRPHSECTYDGKKVVMVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fzvD01 D:4-79    'winged helix' rep  resso              r DNA binding domai3fzvD     02 D:80-164,D:272-300 Periplasmic binding protein-like II                  -3fzvD03 D:166-271 Periplasmic binding protein-like II                                                     3fzvD02 D:80-164,D:272-300    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh---hhhhhhh..hhhhhhhhh--.....--------------.hhhhhhhhhhhhhhhhhhhhh..-----.....eeeeeeee..hhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhh...eeee........eeeee.......eeeee.........eehhhhhh..eeeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh....eee..............eeeeee.........eeeee.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fzv D   4 YTLRQLKYFVTTVEC---AEASRKLYIAQPSISTAV--LEESF--------------LTPAGARFYRKAQELLRmAHEFEQ-----NDVIAGQIDIGCFETVAPLYLPGLIAGFRQAYPGVEIRIRDGEQQELVQGLTSGRFDLAFLYEHDLDSTIETEPLmPPQRPHALLPEGHRFAGQAQVSLRDLCLEPmILLDVQPSRTYFVSLFEELGLTPNIAFSSPSIEmVRGmVGQGFGFSLLVTRPHSECTYDGKKVVmVDLAEPVSTSGLAAAWLKRAQLTKPARLFVDYCREQLGK 300
                                    13    |   23        33     |  43  |      -       |63        73    |   83|     | 93       103       113       123       133       143       153       163 |     173       183       193  |    203       213       223      |233|      243       253       263       273       283       293       
                                         18  22               39 42  46             61               78-MSE84    90                                                                        165-MSE                        196-MSE                           230-MSE                        261-MSE                                   
                                                                                                                                                                                                                                                                234-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3FZV)

(-) CATH Domains  (2, 12)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q9I6S0_PSEAE | Q9I6S0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    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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