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(-) Description

Title :  CRYSTAL STRUCTURE OF APO (IRON-FREE) TAUD
 
Authors :  J. R. O'Brien, D. J. Schuller, V. S. Yang, B. D. Dillard, W. N. Lanzilotta
Date :  21 Mar 03  (Deposition) - 23 Sep 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Jelly Roll Motif, Alpha Ketoglutarate-Dependent Dioxygenase, Taurine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. O'Brien, D. J. Schuller, V. S. Yang, B. D. Dillard, W. N. Lanzilotta
Substrate-Induced Conformational Changes In Escherichia Coli Taurine/Alpha-Ketoglutarate Dioxygenase And Insight Into The Oligomeric Structure
Biochemistry V. 42 5547 2003
PubMed-ID: 12741810  |  Reference-DOI: 10.1021/BI0341096
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-KETOGLUTARATE-DEPENDENT TAURINE DIOXYGENASE
    Chains: A, B, C, D
    EC Number: 1.14.11.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: 2-AMINOETHANESULFONATE DIOXYGENASE, SULFATE STARVATION-INDUCED PROTEIN 3, SSI3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2TAU3Ligand/Ion2-AMINOETHANESULFONIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2TAU1Ligand/Ion2-AMINOETHANESULFONIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2TAU2Ligand/Ion2-AMINOETHANESULFONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:114 , ARG A:266BINDING SITE FOR RESIDUE CL A 900
2AC2SOFTWARELEU B:114 , THR B:126 , ARG B:266 , HOH B:1064BINDING SITE FOR RESIDUE CL B 901
3AC3SOFTWARELEU D:114 , THR D:126 , ARG D:266BINDING SITE FOR RESIDUE CL D 902
4AC4SOFTWAREHIS A:70 , TYR A:73 , ASN A:95 , ASP A:101 , VAL A:102 , PHE A:104 , PHE A:159 , PHE A:206 , ARG A:270 , HOH A:972 , HOH A:1017BINDING SITE FOR RESIDUE TAU A 952
5AC5SOFTWAREHIS B:70 , TYR B:73 , ASN B:95 , HIS B:99 , ASP B:101 , VAL B:102 , PHE B:159 , ARG B:270 , HOH B:995BINDING SITE FOR RESIDUE TAU B 953
6AC6SOFTWAREHIS C:70 , TYR C:73 , ASN C:95 , HIS C:99 , ASP C:101 , VAL C:102 , PHE C:159 , PHE C:206 , ARG C:270 , HOH C:981 , HOH C:1100BINDING SITE FOR RESIDUE TAU C 954

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:262 -Pro A:263
2Leu B:262 -Pro B:263
3Leu C:262 -Pro C:263
4Leu D:262 -Pro D:263

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1OTJ)

(-) 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:281
 aligned with TAUD_ECOLI | P37610 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:281
                                    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 
           TAUD_ECOLI     2 SERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
               SCOP domains d1otja_ A: Taurine/alpha-ketoglutarate dioxygenase TauD                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1otjA00 A:2-282 Clavaminate synthase-like                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhh...........ee..eeeeeeeee.....................eeeeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeehhhhhhhhhhh..hhhhhhhhhhhhhhh..eeee.eee......eee......eeee.....hhhhhhh.hhhhhhhhhh.eeee......eeeee...eeeee........eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otj A   2 SERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
                                    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 


Chain B from PDB  Type:PROTEIN  Length:279
 aligned with TAUD_ECOLI | P37610 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:279
                                    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         
           TAUD_ECOLI     4 RLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
               SCOP domains d1otjb_ B: Taurine/alpha-ketoglutarate dioxygenase TauD                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1otjB00 B:4-282 Clavaminate synthase-like                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhh...........ee..eeeeeeeee.......................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeee.hhhh.hhhhh..hhhhhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhh.hhhhhhhhhh.eeee......eeeee...eeeee........eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otj B   4 RLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
                                    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         


Chain C from PDB  Type:PROTEIN  Length:280
 aligned with TAUD_ECOLI | P37610 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:280
                                    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
           TAUD_ECOLI     3 ERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
               SCOP domains d1otjc_ C: Taurine/alpha-ketoglutarate dioxygenase TauD                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1otjC00 C:3-282 Clavaminate synthase-like                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhhhh.................eeeee.......................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeehhhhhhhhhhh..hhhhhhhhhhhhhhh..eeee.eee......eee......eeee...hhhhhhhhh.hhhhhhhhhh.eeee......eeeee...eeeee........eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otj C   3 ERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
                                    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


Chain D from PDB  Type:PROTEIN  Length:280
 aligned with TAUD_ECOLI | P37610 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:280
                                    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
           TAUD_ECOLI     3 ERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
               SCOP domains d1otjd_ D: Taurine/alpha-ketoglutarate dioxygenase TauD                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1otjD00 D:3-282 Clavaminate synthase-like                                                                                                                                                                                                                                                CATH domains
           Pfam domains (1) ---TauD-1otjD01 D:6-272                                                                                                                                                                                                                                                       ---------- Pfam domains (1)
           Pfam domains (2) ---TauD-1otjD02 D:6-272                                                                                                                                                                                                                                                       ---------- Pfam domains (2)
           Pfam domains (3) ---TauD-1otjD03 D:6-272                                                                                                                                                                                                                                                       ---------- Pfam domains (3)
           Pfam domains (4) ---TauD-1otjD04 D:6-272                                                                                                                                                                                                                                                       ---------- Pfam domains (4)
         Sec.struct. author ...eeee......eeee........hhhhhhhhhhhhhhhheeee.....hhhhhhhhhhh...........ee..eeeeeeeee.......................eeeeeeee.......eeeeehhhhhhh.hhhhhhhhh..eeeehhhhhhhhhhh...................eeee.eee......eee......eeee...hhhhhhhhh.hhhhhhhhhh.eeee......eeeee...eeeee........eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1otj D   3 ERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALAQRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPSTGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKNPPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQPNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRA 282
                                    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
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (TAUD_ECOLI | P37610)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0000908    taurine dioxygenase activity    Catalysis of the reaction: 2-oxoglutarate + O(2) + taurine = aminoacetaldehyde + CO(2) + succinate + sulfite.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006790    sulfur compound metabolic process    The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1otj
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  TAUD_ECOLI | P37610
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 Related Entries

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

UniProtKB/Swiss-Prot
        TAUD_ECOLI | P37610: 1gqw 1gy9 1os7

(-) Related Entries Specified in the PDB File

1os7 CRYSTAL STRUCTURE OF TAUD WITH IRON, ALPHA-KETOGLUTARATE AND TAURINE BOUND AT PH 7.5