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(-) Description

Title :  APO FORM OF THE Y31V MUTANT DIMERIZATION DOMAIN FRAGMENT OF ESCHERICHIA COLI REGULATORY PROTEIN ARAC
 
Authors :  J. E. Weldon, C. Larkin, R. F. Schleif
Date :  23 Sep 04  (Deposition) - 12 Oct 04  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
Keywords :  Transcription Factor, Coiled-Coil, Jelly Roll, Allostery, Arabinose, Carbohydrate Binding, Arac, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. E. Weldon, M. E. Rodgers, C. Larkin, R. F. Schleif
Structure And Properties Of A Truely Apo Form Of Arac Dimerization Domain.
Proteins V. 66 646 2007
PubMed-ID: 17173282  |  Reference-DOI: 10.1002/PROT.21267

(-) Compounds

Molecule 1 - ARABINOSE OPERON REGULATORY PROTEIN
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ARAC
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   CD 
Biological Unit 3 (2x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 25)

Asymmetric Unit (1, 25)
No.NameCountTypeFull Name
1EDO25Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 13)
No.NameCountTypeFull Name
1EDO13Ligand/Ion1,2-ETHANEDIOL
Biological Unit 3 (1, 8)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN D:60 , ARG D:62 , ALA D:115 , GLU D:144BINDING SITE FOR RESIDUE EDO D 301
02AC2SOFTWARELYS D:58 , GLN D:60 , ILE D:79 , HIS D:81 , HOH D:351BINDING SITE FOR RESIDUE EDO D 302
03AC3SOFTWAREGLU A:124 , ARG B:146BINDING SITE FOR RESIDUE EDO B 303
04AC4SOFTWAREHIS A:129 , ILE A:167 , LEU A:171 , HIS A:172BINDING SITE FOR RESIDUE EDO A 304
05AC5SOFTWARELEU D:40 , GLY D:77 , ARG E:62BINDING SITE FOR RESIDUE EDO D 305
06AC6SOFTWAREMET B:42BINDING SITE FOR RESIDUE EDO B 306
07AC7SOFTWAREVAL D:31 , TRP D:95 , EDO D:311BINDING SITE FOR RESIDUE EDO D 307
08AC8SOFTWARELEU E:10 , ARG E:38 , HOH E:360BINDING SITE FOR RESIDUE EDO E 308
09AC9SOFTWAREARG C:38BINDING SITE FOR RESIDUE EDO C 310
10BC1SOFTWARETHR D:24 , ILE D:36 , ARG D:38 , TYR D:82 , HIS D:93 , TRP D:95 , EDO D:307 , EDO D:315 , HOH D:398BINDING SITE FOR RESIDUE EDO D 311
11BC2SOFTWAREGLU E:106 , TRP E:107 , TYR E:147 , LEU E:150 , HOH E:335 , HOH E:368 , HOH E:370BINDING SITE FOR RESIDUE EDO E 312
12BC3SOFTWAREHOH C:357 , GLU E:169BINDING SITE FOR RESIDUE EDO E 313
13BC4SOFTWAREPHE D:119 , PHE D:120 , ARG D:121 , ILE D:167 , HOH D:337BINDING SITE FOR RESIDUE EDO D 314
14BC5SOFTWARETHR D:24 , ILE D:26 , LEU D:32 , PHE D:34 , ILE D:36 , EDO D:311 , HOH D:374 , HOH D:397BINDING SITE FOR RESIDUE EDO D 315
15BC6SOFTWAREPHE B:15 , ASN B:16 , ALA B:17 , EDO B:317BINDING SITE FOR RESIDUE EDO B 316
16BC7SOFTWAREASN B:16 , EDO B:316BINDING SITE FOR RESIDUE EDO B 317
17BC8SOFTWAREARG A:162 , GLU A:165 , ALA A:166 , EDO A:323BINDING SITE FOR RESIDUE EDO A 318
18BC9SOFTWARETYR D:103 , TRP D:107 , HOH D:356BINDING SITE FOR RESIDUE EDO D 319
19CC1SOFTWAREPRO C:173 , PRO C:174 , MET C:175 , ARG D:99 , PRO D:100BINDING SITE FOR RESIDUE EDO C 321
20CC2SOFTWAREPHE D:35 , VAL D:56 , LYS D:58 , GLU D:63 , PRO D:86BINDING SITE FOR RESIDUE EDO D 322
21CC3SOFTWAREHIS A:129 , EDO A:318BINDING SITE FOR RESIDUE EDO A 323
22CC4SOFTWAREPHE C:120 , ARG C:121 , ILE C:167 , GLU D:106 , ASN D:109BINDING SITE FOR RESIDUE EDO D 324
23CC5SOFTWAREHOH D:388 , GLU E:87BINDING SITE FOR RESIDUE EDO E 325

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XJA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XJA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XJA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XJA)

(-) Exons   (0, 0)

(no "Exon" information available for 1XJA)

(-) 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:165
 aligned with ARAC_ECOLI | P0A9E0 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:165
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     
           ARAC_ECOLI     8 PLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLH 172
               SCOP domains d1xjaa_ A: Regulatory protein AraC                                                                                                                                    SCOP domains
               CATH domains 1xjaA00 A:8-172  [code=2.60.120.280, no name defined]                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeee.......eeee......eeeeeeeee.eeeee..eeeee....eeee.....eeeee.....eeeeeeeee..hhhhhhhh...eee..eeee.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xja A   8 PLLPGYSFNAHLVAGLTPIEANGVLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLH 172
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167     


Chain B from PDB  Type:PROTEIN  Length:154
 aligned with ARAC_ECOLI | P0A9E0 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:154
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    
           ARAC_ECOLI    15 FNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAIN 168
               SCOP domains d1xjab_ B: Regulatory protein AraC                                                                                                                         SCOP domains
               CATH domains 1xjaB00 B:15-168  [code=2.60.120.280, no name defined]                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.......eeee......eeeeeeeee.eeeee..eeeee....eeee.....eeeee.....eeeeeeeee..hhhhhhhhh..eee..eeee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xja B  15 FNAHLVAGLTPIEANGVLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAIN 168
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164    


Chain C from PDB  Type:PROTEIN  Length:169
 aligned with ARAC_ECOLI | P0A9E0 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         
           ARAC_ECOLI     7 DPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPM 175
               SCOP domains d1xjac_ C: Regulatory protein AraC                                                                                                                                        SCOP domains
               CATH domains 1xjaC00 C:7-175  [code=2.60.120.280, no name defined]                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeee.......eeee......eeeeeeeee.eeeee..eeeee....eeee.....eeeee.....eeeeeeeee..hhhhhhhhh..eee..eeee.....hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xja C   7 DPLLPGYSFNAHLVAGLTPIEANGVLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPM 175
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166         


Chain D from PDB  Type:PROTEIN  Length:165
 aligned with ARAC_ECOLI | P0A9E0 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:165
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166     
           ARAC_ECOLI     7 DPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESL 171
               SCOP domains d1xjad_ D: Regulatory protein AraC                                                                                                                                    SCOP domains
               CATH domains 1xjaD00 D:7-171  [code=2.60.120.280, no name defined]                                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeee........eee......eeeeeeeee.eeeee..eeeee....eeee.....eeeee.....eeeeeeeee..hhhhhhhh...eee..eeee.....hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xja D   7 DPLLPGYSFNAHLVAGLTPIEANGVLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESL 171
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166     


Chain E from PDB  Type:PROTEIN  Length:163
 aligned with ARAC_ECOLI | P0A9E0 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:163
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166   
           ARAC_ECOLI     7 DPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINE 169
               SCOP domains d1xjae_ E: Regulatory protein AraC                                                                                                                                  SCOP domains
               CATH domains 1xjaE00 E:7-169  [code=2.60.120.280, no name defined]                                                                                                               CATH domains
           Pfam domains (1) -------------AraC_binding-1xjaE01 E:20-160                                                                                                                --------- Pfam domains (1)
           Pfam domains (2) -------------AraC_binding-1xjaE02 E:20-160                                                                                                                --------- Pfam domains (2)
           Pfam domains (3) -------------AraC_binding-1xjaE03 E:20-160                                                                                                                --------- Pfam domains (3)
           Pfam domains (4) -------------AraC_binding-1xjaE04 E:20-160                                                                                                                --------- Pfam domains (4)
           Pfam domains (5) -------------AraC_binding-1xjaE05 E:20-160                                                                                                                --------- Pfam domains (5)
         Sec.struct. author ............eeeeeeeee.......eeee......eeeeeeeee.eeeee..eeeee....eeee.....eeeee.....eeeeeeeee..hhhhhhhhh........eee.....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xja E   7 DPLLPGYSFNAHLVAGLTPIEANGVLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINE 169
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166
   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, 5)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 5)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 5)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (ARAC_ECOLI | P0A9E0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000987    core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon.
    GO:0019172    glyoxalase III activity    Catalysis of the reaction: methylglyoxal + H2O = D-lactate.
    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).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0019568    arabinose catabolic process    The chemical reactions and pathways resulting in the breakdown of arabinose, arabino-pentose.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019243    methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione    The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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  1xja
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARAC_ECOLI | P0A9E0: 2aac 2ara 2arc 2k9s

(-) Related Entries Specified in the PDB File

2aac WILD-TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH D-FUCOSE
2ara WILD-TYPE APO FORM OF THE SAME PROTEIN
2arc WILD-TYPE FORM OF THE SAME PROTEIN COMPLEXED WITH L- ARABINOSE
2k9s