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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CONSERVED HYPOTHETICAL PROTEIN TT1465 FROM THERMUS THERMOPHILUS HB8
 
Authors :  M. Kukimoto-Niino, K. Murayama, M. Kato-Murayama, T. Terada, M. Shiro S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  25 May 04  (Deposition) - 25 Nov 04  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rossmann Fold, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kukimoto-Niino, K. Murayama, M. Kato-Murayama, M. Idaka, Y. Bessho, A. Tatsuguchi, R. Ushikoshi-Nakayama, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structures Of Possible Lysine Decarboxylases From Thermus Thermophilus Hb8
Protein Sci. V. 13 3038 2004
PubMed-ID: 15459330  |  Reference-DOI: 10.1110/PS.041012404

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN TT1465
    Chains: A, B, C, D, E, F
    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
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric/Biological Unit (2, 18)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PO412Ligand/IonPHOSPHATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:45 , ALA A:46 , GLY A:140 , GLY A:141 , PHE A:142 , GLY A:143 , THR A:144 , HOH A:507 , HOH A:545 , HOH B:519 , HOH B:520BINDING SITE FOR RESIDUE PO4 A 501
02AC2SOFTWAREHOH E:516 , PHE F:43 , SER F:45 , ALA F:46 , GLY F:140 , GLY F:141 , PHE F:142 , GLY F:143 , THR F:144 , HOH F:524 , HOH F:536BINDING SITE FOR RESIDUE PO4 F 502
03AC3SOFTWAREHOH A:531 , GLY B:44 , SER B:45 , ALA B:46 , MSE B:81 , GLY B:141 , PHE B:142 , GLY B:143 , THR B:144 , HOH B:508 , HOH B:511 , HOH B:523 , HOH B:544BINDING SITE FOR RESIDUE PO4 B 503
04AC4SOFTWARESER E:45 , ALA E:46 , GLY E:141 , PHE E:142 , GLY E:143 , THR E:144 , HOH E:525 , HOH E:539 , HOH E:547 , HOH E:571BINDING SITE FOR RESIDUE PO4 E 504
05AC5SOFTWARESER C:45 , ALA C:46 , GLY C:141 , PHE C:142 , GLY C:143 , THR C:144 , HOH C:557 , HOH C:558 , HOH D:518 , HOH D:522BINDING SITE FOR RESIDUE PO4 C 505
06AC6SOFTWAREHOH C:542 , PHE D:43 , SER D:45 , ALA D:46 , GLY D:140 , GLY D:141 , PHE D:142 , GLY D:143 , THR D:144 , HOH D:527 , HOH D:537 , HOH D:547BINDING SITE FOR RESIDUE PO4 D 506
07AC7SOFTWAREPHE C:29 , SER C:33 , ARG C:130 , TYR C:131 , HIS D:11 , HIS D:12 , HOH D:546BINDING SITE FOR RESIDUE PO4 C 507
08AC8SOFTWAREHIS C:12 , GLU D:30 , GLU D:34 , HOH D:548 , TRP E:16 , ARG E:17BINDING SITE FOR RESIDUE PO4 D 508
09AC9SOFTWAREHIS E:11 , HIS E:12 , HOH E:517 , PHE F:29 , SER F:33 , TYR F:131BINDING SITE FOR RESIDUE PO4 E 509
10BC1SOFTWAREARG E:130 , TYR E:131 , HIS F:11 , HIS F:12 , HOH F:519BINDING SITE FOR RESIDUE PO4 F 510
11BC2SOFTWARELEU C:10 , HIS C:11 , HIS C:12 , GLU C:13 , HOH C:552 , ARG D:130BINDING SITE FOR RESIDUE PO4 C 511
12BC3SOFTWAREGLN D:9 , TRP D:16 , ARG D:17 , GLU E:30 , GLU E:34 , HOH E:544 , HIS F:12BINDING SITE FOR RESIDUE PO4 D 512

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1WEK)

(-) 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:208
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:208
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204        
         Q5SHT6_THET8     5 PLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
               SCOP domains d1weka_ A: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhh...eeeeee.............eeeee.hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.....hhhhhheee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek A   5 PLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
                                    14        24        34        44        54        64        74      | 84        94       104       114       124       134       144       154       164       174       184       194       204        
                                                                                                       81-MSE                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:207
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
         Q5SHT6_THET8     6 LIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
               SCOP domains d1wekb_ B: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh...eeeeee.............eeeee.hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.....hhhhhheee.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek B   6 LIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
                                    15        25        35        45        55        65        75     |  85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                                                                      81-MSE                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:206
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:211
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211 
         Q5SHT6_THET8     2 PKKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
               SCOP domains d1wekc_ C: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh....eeeeee..-----......eeeee.hhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.....hhhh.eeee.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek C   2 PKKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNIEL-----PNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKA 212
                                    11        21        31        41        51        61        71        81        91       101|     |111       121       131       141       151       161       171       181       191       201       211 
                                                                                                          81-MSE              102   108                                                                                                        


Chain D from PDB  Type:PROTEIN  Length:208
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         Q5SHT6_THET8     3 KKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAP 215
               SCOP domains d1wekd_ D: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh....eeeeee..-----......eeeee.hhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.....hhhhhheee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek D   3 KKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNIEL-----PNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAP 215
                                    12        22        32        42        52        62        72        82        92       102     | 112       122       132       142       152       162       172       182       192       202       212   
                                                                                                         81-MSE              102   108                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:206
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:212
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213  
         Q5SHT6_THET8     4 KPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAP 215
               SCOP domains d1weke_ E: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh....eeeeee.------......eeeee.hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.......eeee....hhhhhhhhhhhhhhh.....hhh.eeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek E   4 KPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNIE------PNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAEAP 215
                                    13        23        33        43        53        63        73       |83        93       | -    |  113       123       133       143       153       163       173       183       193       203       213  
                                                                                                        81-MSE             101    108                                                                                                           


Chain F from PDB  Type:PROTEIN  Length:205
 aligned with Q5SHT6_THET8 | Q5SHT6 from UniProtKB/TrEMBL  Length:217

    Alignment length:212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211  
         Q5SHT6_THET8     2 PKKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVMEAVNRGAYEAGGVSVGLNIELPHEQKPNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAE 213
               SCOP domains d1wekf_ F: Hypothetical protein TT1465 (TTHA1644)                                                                                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F01 F:81-210                                                                                           --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F02 F:81-210                                                                                           --- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F03 F:81-210                                                                                           --- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F04 F:81-210                                                                                           --- Pfam domains (4)
           Pfam domains (5) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F05 F:81-210                                                                                           --- Pfam domains (5)
           Pfam domains (6) -------------------------------------------------------------------------------Lysine_decarbox-1wek       F06 F:81-210                                                                                           --- Pfam domains (6)
         Sec.struct. author ....hhhhh....hhhhhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh...eeeee.-------......eeee..hhhhhhhhhhhheeeeee...hhhhhhhhhhhhhhhhh.......eeeehhhhhhhhhhhhhhhhhh.....hhhh.eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wek F   2 PKKPLIDQLHHEDSWRLFRILAEFVEGFETLSELQVPLVSVFGSARFGEGHPAYEAGYRLGRALAEAGFGVVTGGGPGVmEAVNRGAYEAGGVSVGLNI-------PNPYQTHALSLRYFFVRKVLFVRYAVGFVFLPGGFGTLDELSEVLVLLQTEKVHRFPVFLLDRGYWEGLVRWLAFLRDQKAVGPEDLQLFRLTDEPEEVVQALKAE 213
                                    11        21        31        41        51        61        71        81        91        |-      |111       121       131       141       151       161       171       181       191       201       211  
                                                                                                          81-MSE            100     108
   Legend:   → Mismatch (orange background)
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    → 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, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WEK)

(-) Pfam Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Clan: DprA (10)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q5SHT6_THET8 | Q5SHT6)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
biological process
    GO:0009691    cytokinin biosynthetic process    The chemical reactions and pathways resulting in the formation of cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.

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