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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE THIAMINASE II (SE1693) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 1.65 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Jun 10  (Deposition) - 28 Jul 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Putative Thiaminase-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Putative Thiaminase Ii (Se1693) From Staphylococcus Epidermidis Atcc 12228 At 1. 65 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL ACTIVATOR TENA
    Chains: A, B, C, D
    EC Number: 3.5.99.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TENA, SE_1693
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS
    Organism Taxid: 176280
    Strain: ATCC 12228
    Synonym: PUTATIVE THIAMINASE-2, THIAMINASE II

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 65)

Asymmetric/Biological Unit (6, 65)
No.NameCountTypeFull Name
1ACT6Ligand/IonACETATE ION
2IMD4Ligand/IonIMIDAZOLE
3MPD7Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
5MSE44Mod. Amino AcidSELENOMETHIONINE
6SO41Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:44 , TYR A:47 , TYR A:113 , CYS A:137 , TYR A:141 , GLU A:208 , PHE A:211BINDING SITE FOR RESIDUE IMD A 300
02AC2SOFTWARETHR A:52 , MSE A:78 , MSE C:65BINDING SITE FOR RESIDUE ACT A 318
03AC3SOFTWAREARG A:124 , HOH A:867BINDING SITE FOR RESIDUE ACT A 319
04AC4SOFTWAREASP B:44 , TYR B:47 , CYS B:137 , TYR B:141 , GLU B:208 , PHE B:211BINDING SITE FOR RESIDUE IMD B 301
05AC5SOFTWAREGLU A:50 , ASN A:53 , TRP A:106 , TYR A:118 , ARG B:124 , HOH B:785 , HOH B:887 , HOH C:665BINDING SITE FOR RESIDUE MPD B 310
06AC6SOFTWARELEU B:48 , MSE B:78 , CYS B:137 , TYR B:167 , LEU B:174BINDING SITE FOR RESIDUE MPD B 313
07AC7SOFTWAREASP C:44 , PHE C:51 , CYS C:137 , TYR C:141 , GLU C:208 , PHE C:211BINDING SITE FOR RESIDUE IMD C 303
08AC8SOFTWAREPHE A:122 , MSE C:57 , LYS C:61 , ALA C:121 , HOH C:982BINDING SITE FOR RESIDUE MRD C 304
09AC9SOFTWAREPRO A:60 , HOH A:618 , TYR C:118 , HOH C:1036 , PHE D:119 , ARG D:124BINDING SITE FOR RESIDUE MRD C 305
10BC1SOFTWAREPRO C:108 , SER C:109 , HIS C:112 , HOH C:839 , HOH C:875 , HOH C:991 , HOH C:1011 , PRO D:108 , SER D:109 , HIS D:112BINDING SITE FOR RESIDUE MPD C 306
11BC2SOFTWARESER C:109 , HIS C:210 , ASN C:213 , MSE C:214 , GLU C:219 , HOH C:1085 , MPD D:309BINDING SITE FOR RESIDUE MPD C 307
12BC3SOFTWAREARG C:124 , TYR D:118BINDING SITE FOR RESIDUE ACT C 314
13BC4SOFTWARETYR C:55 , MSE C:134BINDING SITE FOR RESIDUE SO4 C 320
14BC5SOFTWAREASP D:44 , PHE D:51 , TYR D:141 , GLU D:208 , PHE D:211BINDING SITE FOR RESIDUE IMD D 302
15BC6SOFTWARELEU D:48 , TYR D:141 , TYR D:167 , MSE D:171 , MPD D:312 , HOH D:930 , HOH D:966BINDING SITE FOR RESIDUE MRD D 308
16BC7SOFTWAREMPD C:307 , SER D:109 , HIS D:210 , ASN D:213 , MSE D:214 , GLU D:219 , ACT D:315BINDING SITE FOR RESIDUE MPD D 309
17BC8SOFTWAREMSE D:57 , LYS D:61 , ALA D:121 , PHE D:122 , HOH D:1038BINDING SITE FOR RESIDUE MPD D 311
18BC9SOFTWARETYR D:55 , MSE D:78 , MSE D:134 , CYS D:137 , MRD D:308BINDING SITE FOR RESIDUE MPD D 312
19CC1SOFTWAREARG D:209 , HIS D:210 , MPD D:309 , HOH D:553BINDING SITE FOR RESIDUE ACT D 315
20CC2SOFTWAREPHE C:119 , GLU D:50 , HOH D:1039BINDING SITE FOR RESIDUE ACT D 316
21CC3SOFTWARELYS A:31 , SER D:33 , ASN D:34 , HOH D:419BINDING SITE FOR RESIDUE ACT D 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NO6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NO6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NO6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NO6)

(-) Exons   (0, 0)

(no "Exon" information available for 3NO6)

(-) 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:235
 aligned with TENA_STAES | Q8CNK1 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:235
                                    1                                                                                                                                                                                                                                  
                                    |2        12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
           TENA_STAES     - --------MTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAMLIPKMSSMEDVKFLVEQIEFMLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHMYFNAFARENAAFTIAAMAPCPYVYAVIGKRAMEDPKLNKESVTSKWFQFYSTEMDELVDVFDQLMDRLTKHCSETEKKEIKENFLQSTIHERHFFNMAYINEKWEYGGNN 227
               SCOP domains d3no6a_ A: automated matches                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no6 A  -7 HENLYFQGmTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAmLIPKmSSmEDVKFLVEQIEFmLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHmYFNAFARENAAFTIAAmAPCPYVYAVIGKRAmEDPKLNKESVTSKWFQFYSTEmDELVDVFDQLmDRLTKHCSETEKKEIKENFLQSTIHERHFFNmAYINEKWEYGGNN 227
                                    |2        12        22        32        42        52    |   62  |     72     |  82        92       102       112    |  122       132 |     142      |152       162       172       182       192       202       212 |     222     
                                    1-MSE                                                  57-MSE|  |           78-MSE                                117-MSE          134-MSE        149-MSE               171-MSE    182-MSE                         214-MSE         
                                                                                                62-MSE                                                                                                                                                                 
                                                                                                   65-MSE                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with TENA_STAES | Q8CNK1 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           TENA_STAES     1 MTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAMLIPKMSSMEDVKFLVEQIEFMLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHMYFNAFARENAAFTIAAMAPCPYVYAVIGKRAMEDPKLNKESVTSKWFQFYSTEMDELVDVFDQLMDRLTKHCSETEKKEIKENFLQSTIHERHFFNMAYINEKWEYGGN 226
               SCOP domains d3no6b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no6 B   1 mTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAmLIPKmSSmEDVKFLVEQIEFmLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHmYFNAFARENAAFTIAAmAPCPYVYAVIGKRAmEDPKLNKESVTSKWFQFYSTEmDELVDVFDQLmDRLTKHCSETEKKEIKENFLQSTIHERHFFNmAYINEKWEYGGN 226
                            |       10        20        30        40        50      | 60 |  |   70       |80        90       100       110      |120       130   |   140       150       160       170|      180 |     190       200       210   |   220      
                            1-MSE                                                  57-MSE|  |           78-MSE                                117-MSE          134-MSE        149-MSE               171-MSE    182-MSE                         214-MSE        
                                                                                        62-MSE                                                                                                                                                                
                                                                                           65-MSE                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:226
 aligned with TENA_STAES | Q8CNK1 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
           TENA_STAES     1 MTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAMLIPKMSSMEDVKFLVEQIEFMLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHMYFNAFARENAAFTIAAMAPCPYVYAVIGKRAMEDPKLNKESVTSKWFQFYSTEMDELVDVFDQLMDRLTKHCSETEKKEIKENFLQSTIHERHFFNMAYINEKWEYGGN 226
               SCOP domains d3no6c_ C: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no6 C   1 mTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAmLIPKmSSmEDVKFLVEQIEFmLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHmYFNAFARENAAFTIAAmAPCPYVYAVIGKRAmEDPKLNKESVTSKWFQFYSTEmDELVDVFDQLmDRLTKHCSETEKKEIKENFLQSTIHERHFFNmAYINEKWEYGGN 226
                            |       10        20        30        40        50      | 60 |  |   70       |80        90       100       110      |120       130   |   140       150       160       170|      180 |     190       200       210   |   220      
                            1-MSE                                                  57-MSE|  |           78-MSE                                117-MSE          134-MSE        149-MSE               171-MSE    182-MSE                         214-MSE        
                                                                                        62-MSE                                                                                                                                                                
                                                                                           65-MSE                                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:227
 aligned with TENA_STAES | Q8CNK1 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
           TENA_STAES     1 MTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAMLIPKMSSMEDVKFLVEQIEFMLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHMYFNAFARENAAFTIAAMAPCPYVYAVIGKRAMEDPKLNKESVTSKWFQFYSTEMDELVDVFDQLMDRLTKHCSETEKKEIKENFLQSTIHERHFFNMAYINEKWEYGGNN 227
               SCOP domains d3no6d_ D: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------TENA_THI-4-3no6D01 D:8-218                                                                                                                                                                                         --------- Pfam domains (1)
           Pfam domains (2) -------TENA_THI-4-3no6D02 D:8-218                                                                                                                                                                                         --------- Pfam domains (2)
           Pfam domains (3) -------TENA_THI-4-3no6D03 D:8-218                                                                                                                                                                                         --------- Pfam domains (3)
           Pfam domains (4) -------TENA_THI-4-3no6D04 D:8-218                                                                                                                                                                                         --------- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3no6 D   1 mTFSKELREASRPIIDDIYNDGFIQDLLAGKLSNQAVRQYLRADASYLKEFTNIYAmLIPKmSSmEDVKFLVEQIEFmLEGEVEAHEVLADFINEPYEEIVKEKVWPPSGDHYIKHmYFNAFARENAAFTIAAmAPCPYVYAVIGKRAmEDPKLNKESVTSKWFQFYSTEmDELVDVFDQLmDRLTKHCSETEKKEIKENFLQSTIHERHFFNmAYINEKWEYGGNN 227
                            |       10        20        30        40        50      | 60 |  |   70       |80        90       100       110      |120       130   |   140       150       160       170|      180 |     190       200       210   |   220       
                            1-MSE                                                  57-MSE|  |           78-MSE                                117-MSE          134-MSE        149-MSE               171-MSE    182-MSE                         214-MSE         
                                                                                        62-MSE                                                                                                                                                                 
                                                                                           65-MSE
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NO6)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: HO (49)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (TENA_STAES | Q8CNK1)
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: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:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
    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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