2V8U - JenaLib

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Title :   ATOMIC RESOLUTION STRUCTURE OF MN CATALASE FROM THERMUS THERMOPHILUS

Authors :   V. V. Barynin, S. V. Antonyuk, A. A. Vaguine, W. R. Melik-Adamyan, A. N. Popov, V. S. Lamsin, P. M. Harrison, P. J. Artymiuk

Date :   14 Aug 07 (Deposition) - 25 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

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

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

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (3x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 26)

No.	Name	Count	Type	Full Name
1	LI	5	Ligand/Ion	LITHIUM ION
2	MN	4	Ligand/Ion	MANGANESE (II) ION
3	O	10	Ligand/Ion	OXYGEN ATOM
4	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 21)

No.	Name	Count	Type	Full Name
1	LI	-1	Ligand/Ion	LITHIUM ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	O	-1	Ligand/Ion	OXYGEN ATOM
4	SO4	21	Ligand/Ion	SULFATE ION

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:36 , GLU A:70 , HIS A:73 , MN A:1304 , O A:1305 , O A:1306 , O A:1307 , O A:1308 , O A:1309	BINDING SITE FOR RESIDUE MN A1303
02	AC2	SOFTWARE	GLU A:70 , GLU A:155 , HIS A:188 , MN A:1303 , O A:1305 , O A:1306 , O A:1307 , O A:1308	BINDING SITE FOR RESIDUE MN A1304
03	AC3	SOFTWARE	GLU A:70 , HIS A:73 , HIS A:188 , MN A:1303 , MN A:1304 , O A:1306 , O A:1307 , O A:1308 , O A:1309 , HOH A:2531	BINDING SITE FOR RESIDUE O A1305
04	AC4	SOFTWARE	GLU A:36 , THR A:39 , GLU A:70 , GLU A:155 , MN A:1303 , MN A:1304 , O A:1305 , O A:1307 , O A:1308 , O A:1309	BINDING SITE FOR RESIDUE O A1306
05	AC5	SOFTWARE	GLU A:36 , GLU A:70 , HIS A:73 , GLU A:155 , HIS A:188 , MN A:1303 , MN A:1304 , O A:1305 , O A:1306 , O A:1308 , O A:1309 , HOH A:2529 , HOH A:2531	BINDING SITE FOR RESIDUE O A1307
06	AC6	SOFTWARE	GLU A:36 , THR A:39 , LYS A:162 , MN A:1303 , MN A:1304 , O A:1305 , O A:1306 , O A:1307 , O A:1309 , HOH A:2529 , HOH A:2530	BINDING SITE FOR RESIDUE O A1308
07	AC7	SOFTWARE	GLU A:36 , HIS A:73 , LYS A:162 , LEU A:181 , MN A:1303 , O A:1305 , O A:1306 , O A:1307 , O A:1308 , HOH A:2529 , HOH A:2531	BINDING SITE FOR RESIDUE O A1309
08	AC8	SOFTWARE	ASP A:19 , HOH A:2053 , HOH A:2060 , HOH A:2533	BINDING SITE FOR RESIDUE LI A1310
09	AC9	SOFTWARE	ASP A:240 , HOH A:2127 , HOH A:2164 , HOH A:2410 , HOH A:2416	BINDING SITE FOR RESIDUE LI A1311
10	BC1	SOFTWARE	PRO A:15 , LYS A:16 , ASN A:171 , PRO A:172 , HOH A:2318 , HOH A:2532 , HOH A:2533 , HOH A:2534 , HOH A:2535 , HOH A:2536	BINDING SITE FOR RESIDUE SO4 A1312
11	BC2	SOFTWARE	PHE A:229 , PRO A:266 , THR A:267 , GLY A:268 , HOH A:2402 , HOH A:2538 , HOH A:2539 , HOH A:2540 , HOH A:2541 , HOH A:2542 , ARG B:7	BINDING SITE FOR RESIDUE SO4 A1313
12	BC3	SOFTWARE	HOH A:2392 , HOH A:2447 , HOH A:2554	BINDING SITE FOR RESIDUE LI A1314
13	BC4	SOFTWARE	LYS A:54 , THR A:257 , GLU A:258 , HOH A:2455 , HOH A:2544 , HOH A:2546 , HOH A:2547 , HOH A:2553	BINDING SITE FOR RESIDUE SO4 A1315
14	BC5	SOFTWARE	LYS A:54 , ARG A:231 , HOH A:2548 , HOH A:2549 , HOH A:2550 , HOH A:2551 , HOH A:2552 , HOH A:2553 , HOH A:2554 , HOH A:2555	BINDING SITE FOR RESIDUE SO4 A1316
15	BC6	SOFTWARE	LEU B:12 , HOH B:2032 , HOH B:2037	BINDING SITE FOR RESIDUE LI B1303
16	BC7	SOFTWARE	GLN B:9 , ILE B:10 , TYR B:180 , HOH B:2024 , HOH B:2310	BINDING SITE FOR RESIDUE LI B1304
17	BC8	SOFTWARE	LYS B:194 , GLY B:250 , ALA B:251 , HOH B:2318 , HOH B:2505 , HOH B:2506 , HOH B:2507 , HOH B:2508 , HOH B:2509 , HOH B:2510	BINDING SITE FOR RESIDUE SO4 B1305
18	BC9	SOFTWARE	GLU B:36 , GLU B:70 , HIS B:73 , MN B:1307 , O B:1308 , O B:1309 , O B:1310 , O B:1311 , O B:1312	BINDING SITE FOR RESIDUE MN B1306
19	CC1	SOFTWARE	GLU B:70 , GLU B:155 , HIS B:188 , MN B:1306 , O B:1308 , O B:1309 , O B:1310 , O B:1311	BINDING SITE FOR RESIDUE MN B1307
20	CC2	SOFTWARE	GLU B:70 , HIS B:73 , GLY B:185 , HIS B:188 , MN B:1306 , MN B:1307 , O B:1309 , O B:1310 , O B:1311 , O B:1312 , HOH B:2511	BINDING SITE FOR RESIDUE O B1308
21	CC3	SOFTWARE	GLU B:36 , THR B:39 , GLU B:70 , GLU B:155 , MN B:1306 , MN B:1307 , O B:1308 , O B:1310 , O B:1311 , O B:1312	BINDING SITE FOR RESIDUE O B1309
22	CC4	SOFTWARE	GLU B:36 , GLU B:70 , HIS B:73 , GLU B:155 , HIS B:188 , MN B:1306 , MN B:1307 , O B:1308 , O B:1309 , O B:1311 , O B:1312 , HOH B:2295 , HOH B:2511	BINDING SITE FOR RESIDUE O B1310
23	CC5	SOFTWARE	GLU B:36 , THR B:39 , LYS B:162 , MN B:1306 , MN B:1307 , O B:1308 , O B:1309 , O B:1310 , O B:1312 , HOH B:2105 , HOH B:2295	BINDING SITE FOR RESIDUE O B1311
24	CC6	SOFTWARE	GLU B:36 , HIS B:73 , LYS B:162 , LEU B:181 , MN B:1306 , O B:1308 , O B:1309 , O B:1310 , O B:1311 , HOH B:2295 , HOH B:2511	BINDING SITE FOR RESIDUE O B1312
25	CC7	SOFTWARE	LYS A:222 , MET B:14 , HOH B:2512 , HOH B:2513 , HOH B:2516 , HOH B:2517 , HOH B:2518 , HOH B:2519	BINDING SITE FOR RESIDUE SO4 B1313
26	CC8	SOFTWARE	LYS B:57 , GLU B:239 , TYR B:241 , ARG B:242 , HOH B:2402 , HOH B:2520 , HOH B:2522	BINDING SITE FOR RESIDUE SO4 B1314

(no "SS Bond" information available for 2V8U)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2V8U)

(no "PROSITE Motif" information available for 2V8U)

(no "Exon" information available for 2V8U)

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 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 d2v8ua_ 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
                 2v8u 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 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 d2v8ub_ B: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Mn_catalase-2v8uB01 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) Mn_catalase-2v8uB02 B:1-302                                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author .eee..ee..........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh.hhhhhhh..hhhhhh................hhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhh.eeee.......hhhhh............eeee.....ee.......hhhh.....hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v8u 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Ferritin-like (533)

Superfamily: Ferritin-like (489)

Family: Manganese catalase (T-catalase) (7)

Protein domain: automated matches (3)

Thermus thermophilus [TaxId: 262724] (2)

1a	d2v8ua_	A:
1b	d2v8ub_	B:

(no "CATH Domain" information available for 2V8U)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ferritin (185)

Family: Mn_catalase (2)

Thermus thermophilus (2)

1a	Mn_catalase-2v8uB01	B:1-302
1b	Mn_catalase-2v8uB02	B:1-302

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.

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	Cis Peptide Bonds
		Ala A:282 - Pro A:283	[ RasMol ]
		Ala B:282 - Pro B:283	[ RasMol ]
		Ile A:210 - Pro A:211	[ RasMol ]
		Ile B:210 - Pro B:211	[ RasMol ]
		Leu A:208 - Pro A:209	[ RasMol ]
		Leu B:208 - Pro B:209	[ RasMol ]

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2cwl	CRYSTAL STRUCTURE OF MANGANESE-FREE FORM OF PSEUDOCATALASEFROM THERMUS THERMOPHILUS HB8
2v8t	CRYSTAL STRUCTURE OF MN CATALASE FROM THERMUS THERMOPHILUS COMPLEXED WITH CLORIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (26, 26)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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