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(-) Description

Title :  CRYSTAL STRUCTURE OF A TENA FAMILY TRANSCRIPTION REGULATOR (TM1040_3656) FROM SILICIBACTER SP. TM1040 AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  04 May 10  (Deposition) - 26 May 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Tena/Thi-4/Pqqc Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transcription, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Tena Family Transcription Regulator (Tm1040_3656) From Silicibacter Sp. Tm1040 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TENA FAMILY TRANSCRIPTIONAL REGULATOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1040_3656
    Organism Scientific: RUEGERIA SP. TM1040
    Organism Taxid: 292414

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3IMD1Ligand/IonIMIDAZOLE
4MSE6Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 76)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO48Ligand/Ion1,2-ETHANEDIOL
3IMD4Ligand/IonIMIDAZOLE
4MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:49 , PHE A:52 , CYS A:140 , TYR A:144 , GLU A:215 , PHE A:218 , EDO A:237BINDING SITE FOR RESIDUE IMD A 226
02AC2SOFTWARESER A:71 , THR A:181 , LEU A:182 , ASP A:185 , HOH A:264BINDING SITE FOR RESIDUE EDO A 227
03AC3SOFTWAREARG A:58 , VAL A:65 , LYS A:66 , SER A:67 , ARG A:203 , EDO A:235BINDING SITE FOR RESIDUE EDO A 228
04AC4SOFTWAREARG A:109 , GLN A:206 , HIS A:209 , THR A:210 , GLU A:213 , EDO A:230 , EDO A:234 , HOH A:294BINDING SITE FOR RESIDUE EDO A 229
05AC5SOFTWAREARG A:109 , ALA A:112 , THR A:210 , GLU A:213 , EDO A:229 , EDO A:233 , HOH A:247 , HOH A:312BINDING SITE FOR RESIDUE EDO A 230
06AC6SOFTWARELYS A:7 , ALA A:193 , GLU A:194 , PHE A:195 , THR A:196BINDING SITE FOR RESIDUE EDO A 231
07AC7SOFTWAREGLU A:68 , ARG A:189 , ARG A:190 , PRO A:199 , ARG A:200 , ARG A:203 , HOH A:248BINDING SITE FOR RESIDUE EDO A 232
08AC8SOFTWAREARG A:109 , ARG A:111 , ALA A:112 , GLU A:113 , EDO A:230BINDING SITE FOR RESIDUE EDO A 233
09AC9SOFTWAREGLU A:15 , GLN A:206 , HIS A:209 , EDO A:229BINDING SITE FOR RESIDUE EDO A 234
10BC1SOFTWAREALA A:124 , ASP A:132 , ARG A:203 , THR A:207 , EDO A:228 , HOH A:306BINDING SITE FOR RESIDUE EDO A 235
11BC2SOFTWAREALA A:112 , GLU A:113 , HOH A:257BINDING SITE FOR RESIDUE EDO A 236
12BC3SOFTWAREGLU A:87 , TYR A:172 , IMD A:226BINDING SITE FOR RESIDUE EDO A 237
13BC4SOFTWAREGLU A:15 , PRO A:18BINDING SITE FOR RESIDUE EDO A 238
14BC5SOFTWAREHIS A:44 , GLN A:48 , HOH A:338BINDING SITE FOR RESIDUE CL A 239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:17 -Pro A:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MVU)

(-) 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:225
 aligned with Q1GL43_RUEST | Q1GL43 from UniProtKB/TrEMBL  Length:225

    Alignment length:225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     
         Q1GL43_RUEST     1 MSEPYGKAFSLMRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKSETHSEMLAAVGTVNALVAEEMQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPCVMGYGEIGKRLTAEATSTLYGDWIDTYGGDDYQAACKAVGTLLDDALERRLGAEFTSSPRWSRLCQTFHTATELEVGFWQMGLTP 225
               SCOP domains d3mvua_ A: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mvu A   1 mSEPYGKAFSLmRAEAEPAWRAYTHHAFVEGLKAGTLPREAFLHYLQQDYVFLIHFSRAWALAVVKSETHSEmLAAVGTVNALVAEEmQLHIGICEASGISQEALFATRERAENLAYTRFVLEAGYSGDLLDLLAALAPCVmGYGEIGKRLTAEATSTLYGDWIDTYGGDDYQAACKAVGTLLDDALERRLGAEFTSSPRWSRLCQTFHTATELEVGFWQmGLTP 225
                            |       10 |      20        30        40        50        60        70  |     80       |90       100       110       120       130       140 |     150       160       170       180       190       200       210       220|    
                            |         12-MSE                                                       73-MSE         88-MSE                                               142-MSE                                                                        221-MSE
                            1-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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MVU)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q1GL43_RUEST | Q1GL43)
molecular function
    GO:0050334    thiaminase activity    Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+).
biological process
    GO:0006772    thiamine metabolic process    The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

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