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(-) Description

Title :  CRYSTAL STRUCTURE OF MN CATALASE FROM THERMUS THERMOPHILUS COMPLEXED WITH CHLORIDE
 
Authors :  S. V. Antonyuk, V. V. Barynin, A. A. Vaguine, W. R. Melik-Adamyan, A. N. Popov, V. S. Lamsin, P. M. Harrison, P. J. Artymiuk
Date :  14 Aug 07  (Deposition) - 11 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.98
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Manganese Catalase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. V. Antonyuk, W. R. Melik-Adamyan, A. N. Popov, V. S. Lamsin, P. D. Hempstead, P. M. Harrison, P. J. Artymyuk, V. V. Barynin
Three-Dimentional Structure Of The Enzyme Dimanganese Catalase From Thermus Thermophilus At 1 Angstrom Resolution
Crystallogr. Rep. (Transl. V. 45 105 2000 Kristallografiya)
PubMed: search

(-) Compounds

Molecule 1 - MANGANESE-CONTAINING PSEUDOCATALASE
    Chains: A, B
    EC Number: 1.11.1.6
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27
    Synonym: DIMANGANESE CATALASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2LI1Ligand/IonLITHIUM ION
3MN4Ligand/IonMANGANESE (II) ION
4SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2LI-1Ligand/IonLITHIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
4SO418Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:36 , GLU A:70 , HIS A:73 , MN A:1304 , CL A:1305 , CL A:1306 , HOH A:2503 , HOH A:2504BINDING SITE FOR RESIDUE MN A1303
02AC2SOFTWAREGLU A:70 , GLU A:155 , HIS A:188 , MN A:1303 , CL A:1305 , CL A:1306 , HOH A:2503BINDING SITE FOR RESIDUE MN A1304
03AC3SOFTWAREHIS A:73 , GLY A:185 , HIS A:188 , MN A:1303 , MN A:1304 , CL A:1306 , HOH A:2503 , HOH A:2504BINDING SITE FOR RESIDUE CL A1305
04AC4SOFTWAREGLU A:36 , THR A:39 , GLU A:70 , GLU A:155 , MN A:1303 , MN A:1304 , CL A:1305 , HOH A:2288 , HOH A:2503BINDING SITE FOR RESIDUE CL A1306
05AC5SOFTWAREPHE A:229 , PRO A:266 , THR A:267 , GLY A:268 , HOH A:2376 , HOH A:2505 , HOH A:2506 , HOH A:2507 , HOH A:2508 , ARG B:7BINDING SITE FOR RESIDUE SO4 A1307
06AC6SOFTWAREPRO A:15 , LYS A:16 , ASN A:171 , PRO A:172 , HOH A:2296 , HOH A:2509 , HOH A:2510 , HOH A:2511 , HOH A:2512 , HOH A:2513BINDING SITE FOR RESIDUE SO4 A1308
07AC7SOFTWAREASP A:19 , HOH A:2036 , HOH A:2042 , HOH A:2052 , HOH A:2512BINDING SITE FOR RESIDUE LI A1309
08AC8SOFTWARELYS B:194 , LYS B:249 , GLY B:250 , ALA B:251 , HOH B:2475 , HOH B:2476 , HOH B:2477 , HOH B:2478 , HOH B:2479 , HOH B:2480BINDING SITE FOR RESIDUE SO4 B1303
09AC9SOFTWAREARG B:242BINDING SITE FOR RESIDUE SO4 B1304
10BC1SOFTWAREGLU B:36 , GLU B:70 , HIS B:73 , MN B:1306 , CL B:1307 , CL B:1308 , HOH B:2481 , HOH B:2482BINDING SITE FOR RESIDUE MN B1305
11BC2SOFTWAREGLU B:70 , GLU B:155 , HIS B:188 , MN B:1305 , CL B:1307 , CL B:1308 , HOH B:2481BINDING SITE FOR RESIDUE MN B1306
12BC3SOFTWAREHIS B:73 , GLY B:185 , HIS B:188 , MN B:1305 , MN B:1306 , CL B:1308 , HOH B:2481 , HOH B:2482BINDING SITE FOR RESIDUE CL B1307
13BC4SOFTWAREGLU B:36 , THR B:39 , GLU B:70 , GLU B:155 , LYS B:162 , MN B:1305 , MN B:1306 , CL B:1307 , HOH B:2481BINDING SITE FOR RESIDUE CL B1308
14BC5SOFTWARELYS B:57 , GLU B:239 , TYR B:241 , ARG B:242 , HOH B:2361 , HOH B:2370 , HOH B:2483 , HOH B:2484BINDING SITE FOR RESIDUE SO4 B1309
15BC6SOFTWAREARG A:231 , HOH A:2367 , HOH A:2368 , HOH A:2515 , HOH A:2516 , HOH A:2518 , HOH A:2520BINDING SITE FOR RESIDUE SO4 A1310

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2V8T)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Leu A:208 -Pro A:209
2Ile A:210 -Pro A:211
3Ala A:282 -Pro A:283
4Leu B:208 -Pro B:209
5Ile B:210 -Pro B:211
6Ala B:282 -Pro B:283

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2V8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2V8T)

(-) Exons   (0, 0)

(no "Exon" information available for 2V8T)

(-) 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:302
 aligned with Q72GH6_THET2 | Q72GH6 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q72GH6_THET2     1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
               SCOP domains d2v8ta_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhh..hhhhhh................hhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.eeee.......hhhhh............eeee.....ee.......hhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8t A   1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  


Chain A from PDB  Type:PROTEIN  Length:302
 aligned with Q84DB4_THETH | Q84DB4 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q84DB4_THETH     1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
               SCOP domains d2v8ta_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..ee..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhh..hhhhhh................hhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.eeee.......hhhhh............eeee.....ee.......hhhh.....hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8t A   1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q72GH6_THET2 | Q72GH6 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q72GH6_THET2     1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
               SCOP domains d2v8tb_ B: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Mn_catalase-2v8tB01 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Mn_catalase-2v8tB02 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author .eee..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhh..hhhhhh................hhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.eeee.......hhhhh............eeee..............hhhh.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8t B   1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q84DB4_THETH | Q84DB4 from UniProtKB/TrEMBL  Length:302

    Alignment length:302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300  
         Q84DB4_THETH     1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
               SCOP domains d2v8tb_ B: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Mn_catalase-2v8tB01 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Mn_catalase-2v8tB02 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author .eee..............hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhh..hhhhhh................hhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.eeee.......hhhhh............eeee..............hhhh.....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8t B   1 MFLRIDRLQIELPMPKEQDPNAAAAVQALLGGRFGEMSTLMNYMYQSFNFRGKKALKPYYDLIANIATEELGHIELVAATINSLLAKNPGKDLEEGVDPASTPLGFAKDVRNAAHFIAGGANSLVMGAMGEHWNGEYVFTSGNLILDLLHNFFLEVAARTHKLRVYEMTDNPVAREMIGYLLVRGGVHAAAYGKALESLTGVEMTKMLPIPKIDNSKIPEAKKYMDLGFHRNLYRFSPEDYRDLGLIWKGASPEDGTEVVVVDGPPTGGPVFDAGHDAAEFAPEFHPGELYEIAKKLYEKAK 302
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2V8T)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Ferritin (185)

(-) Gene Ontology  (6, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q84DB4_THETH | Q84DB4)
molecular function
    GO:0004096    catalase activity    Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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.

Chain A,B   (Q72GH6_THET2 | Q72GH6)
molecular function
    GO:0004096    catalase activity    Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
    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:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    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.

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  2v8t
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  Q84DB4_THETH | Q84DB4
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 Related Entries

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

UniProtKB/TrEMBL
        Q84DB4_THETH | Q84DB4: 2v8u

(-) Related Entries Specified in the PDB File

2cwl CRYSTAL STRUCTURE OF MANGANESE-FREE FORM OF PSEUDOCATALASEFROM THERMUS THERMOPHILUS HB8
2v8u ATOMIC RESOLUTION STRUCTURE OF MN CATALASE FROM THERMUS THERMOPHILUS