1NM0 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   PROTEUS MIRABILIS CATALASE IN COMPLEX WITH FORMIATE

Authors :   P. Andreoletti, A. Pernoud, P. Gouet, H. M. Jouve

Date :   08 Jan 03 (Deposition) - 20 Jan 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (4x)

Keywords :   Alpha+Beta, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Andreoletti, A. Pernoud, G. Sainz, P. Gouet, H. M. Jouve
Structural Studies Of Proteus Mirabilis Catalase In Its Ground State, Oxidized State And In Complex With Formic Acid.
Acta Crystallogr. , Sect. D V. 59 2163 2003
PubMed-ID: 14646074 | Reference-DOI: 10.1107/S0907444903019620

Molecule 1 - CATALASE
	Chains	:	A
	EC Number	:	1.11.1.6
	Organism Scientific	:	PROTEUS MIRABILIS
	Organism Taxid	:	584

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 10)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OMT	1	Mod. Amino Acid	S-DIOXYMETHIONINE
5	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (5, 10)

No.	Name	Count	Type	Full Name
1	FMT	1	Ligand/Ion	FORMIC ACID
2	GOL	1	Ligand/Ion	GLYCEROL
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OMT	1	Mod. Amino Acid	S-DIOXYMETHIONINE
5	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 2 (5, 40)

No.	Name	Count	Type	Full Name
1	FMT	4	Ligand/Ion	FORMIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	OMT	4	Mod. Amino Acid	S-DIOXYMETHIONINE
5	SO4	24	Ligand/Ion	SULFATE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:182 , HIS A:192 , ARG A:216 , HOH A:860	BINDING SITE FOR RESIDUE SO4 A 485
2	AC2	SOFTWARE	ARG A:423 , HOH A:553 , HOH A:843 , HOH A:905	BINDING SITE FOR RESIDUE SO4 A 486
3	AC3	SOFTWARE	SER A:430 , ASP A:432 , ARG A:436	BINDING SITE FOR RESIDUE SO4 A 487
4	AC4	SOFTWARE	ARG A:182 , ASN A:223 , HOH A:841	BINDING SITE FOR RESIDUE SO4 A 488
5	AC5	SOFTWARE	ARG A:216 , GLN A:218	BINDING SITE FOR RESIDUE SO4 A 489
6	AC6	SOFTWARE	ARG A:45 , ARG A:342 , TYR A:343 , HOH A:661	BINDING SITE FOR RESIDUE SO4 A 490
7	AC7	SOFTWARE	ASP A:44 , ARG A:51 , HIS A:54 , ARG A:91 , VAL A:125 , GLY A:126 , ASN A:127 , PRO A:137 , PHE A:140 , GLY A:195 , SER A:196 , HIS A:197 , PHE A:313 , MET A:329 , ARG A:333 , SER A:336 , TYR A:337 , HIS A:341 , ARG A:344 , FMT A:492 , HOH A:494 , HOH A:642 , HOH A:646	BINDING SITE FOR RESIDUE HEM A 491
8	AC8	SOFTWARE	OMT A:53 , HIS A:54 , ASN A:127 , PHE A:132 , PHE A:140 , HEM A:491	BINDING SITE FOR RESIDUE FMT A 492
9	AC9	SOFTWARE	GLU A:38 , HIS A:42 , ARG A:342 , HIS A:349 , HOH A:593 , HOH A:625 , HOH A:696 , HOH A:697	BINDING SITE FOR RESIDUE GOL A 493

(no "SS Bond" information available for 1NM0)

Asymmetric Unit

No.	Residues
1	Glu A:383	-	Pro A:384

(no "SAP(SNP)/Variant" information available for 1NM0)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_PROMI	43-59	1	A:43-59
2	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_PROMI	333-341	1	A:333-341

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_PROMI	43-59	1	A:43-59
2	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_PROMI	333-341	1	A:333-341

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_PROMI	43-59	4	A:43-59
2	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_PROMI	333-341	4	A:333-341

(no "Exon" information available for 1NM0)

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:476
 aligned with CATA_PROMI | P42321 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:476
                                    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       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
           CATA_PROMI     4 KKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRMHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLE 479
               SCOP domains d1nm0a_ A: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---Catalase-1nm0A02 A:7-391                                                                                                                                                                                                                                                                                                                                                                         -------------------Catalase-rel-1nm0A01 A:411-476                                    --- Pfam domains
         Sec.struct. author .............................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh.ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeee.hhhhh...................eeeeeeeeee...hhhhhh.............ee...hhhhhhhhhhhhhhhhhhhh.hhhhh........................................hhhhh.............hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------CATALASE_2       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATALASE_------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nm0 A   4 KKLTTAAGAPVVDNNNVITAGPRGPMLLQDVWFLEKLAHFDREVIPERRmHAKGSGAFGTFTVTHDITKYTRAKIFSEVGKKTEMFARFSTVAGERGAADAERDIRGFALKFYTEEGNWDMVGNNTPVFYLRDPLKFPDLNHIVKRDPRTNMRNMAYKWDFFSHLPESLHQLTIDMSDRGLPLSYRFVHGFGSHTYSFINKDNERFWVKFHFRCQQGIKNLMDDEAEALVGKDRESSQRDLFEAIERGDYPRWKLQIQIMPEKEASTVPYNPFDLTKVWPHADYPLMDVGYFELNRNPDNYFSDVEQAAFSPANIVPGISFSPDKMLQGRLFSYGDAHRYRLGVNHHQIPVNAPKCPFHNYHRDGAMRVDGNSGNGITYEPNSGGVFQEQPDFKEPPLSIEGAADHWNHREDEDYFSQPRALYELLSDDEHQRMFARIAGELSQASKETQQRQIDLFTKVHPEYGAGVEKAIKVLE 479
                                    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       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473      
                                                                            53-OMT

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: Multi-domain proteins (alpha and beta) (2421)

Fold: Heme-dependent catalase-like (82)

Superfamily: Heme-dependent catalase-like (82)

Family: Heme-dependent catalases (80)

Protein domain: Catalase I (32)

Proteus mirabilis [TaxId: 584] (9)

d1nm0a_

(no "CATH Domain" information available for 1NM0)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Catalase-rel] (18)

Family: Catalase-rel (18)

Proteus mirabilis (2)

Catalase-rel-1nm0A01

A:411-476

Clan: no clan defined [family: Catalase] (19)

Family: Catalase (19)

Proteus mirabilis (2)

Catalase-1nm0A02

A:7-391

Asymmetric Unit(hide GO term definitions)

Chain A (CATA_PROMI | P42321)

molecular function
	GO:0004096	catalase activity	Catalysis of the reaction: 2 hydrogen peroxide = O2 + 2 H2O.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	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:0042744	hydrogen peroxide catabolic process	The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).
	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:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Glu A:383 - Pro A:384	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	1nm0
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	1.11.1.6
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	CATA_PROMI \| P42321
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UniProtKB/Swiss-Prot
	CATA_PROMI \| P42321	:	1e93 1h6n 1h7k 1m85 1mqf 2cag 2cah 3hb6

1e93	HIGH RESOLUTION STRUCTURE AND BIOCHEMICAL PROPERTIES OF A RECOMBINANT CATALASE DEPLETED IN IRON
1m85	STRUCTURE OF PROTEUS MIRABILIS CATALASE FOR THE NATIVE FORM
1mqf	COMPOUND I FROM PROTEUS MIRABILIS CATALASE
2cag	CATALASE COMPOUND II
2cah	STRUCTURE OF PROTEUS MIRABILIS PR CATALASE FOR THE NATIVE FORM (E-FE(III)) COMPLEXED WITH NADPH

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 10)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (2, 2)

Gene Ontology (10, 10)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File