2IQF - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HELICOBACTER PYLORI CATALASE COMPOUND I

Authors :   P. C. Loewen, X. Carpena, I. Fita

Date :   13 Oct 06 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

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

Keywords :   Hydroxoferryl Heme, Beta Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Alfonso-Prieto, A. Borovik, X. Carpena, G. Murshudov, W. Melik-Adamyan, I. Fita, C. Rovira, P. C. Loewen
The Structures And Electronic Configuration Of Compound I Intermediates Of Helicobacter Pylori And Penicillium Vitale Catalases Determined By X-Ray Crystallography And Qm/Mm Density Functional Theory Calculations.
J. Am. Chem. Soc. V. 129 4193 2007
PubMed-ID: 17358056 | Reference-DOI: 10.1021/JA063660Y
(for further references see the PDB file header)

Molecule 1 - CATALASE
	Chains	:	A, B
	EC Number	:	1.11.1.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSO100
	Expression System Strain	:	UM255
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KATA
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MHO	8	Mod. Amino Acid	S-OXYMETHIONINE
4	O	2	Ligand/Ion	OXYGEN ATOM

Biological Unit 1 (3, 22)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
3	MHO	16	Mod. Amino Acid	S-OXYMETHIONINE
4	O	-1	Ligand/Ion	OXYGEN ATOM

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:47 , TYR A:345 , HOH A:1336 , ARG B:47 , ARG B:344 , TYR B:345	BINDING SITE FOR RESIDUE ACT A 900
2	AC2	SOFTWARE	LEU A:42 , ASP A:46 , ARG A:53 , VAL A:54 , VAL A:55 , HIS A:56 , ARG A:93 , GLY A:112 , VAL A:127 , GLY A:128 , ASN A:129 , ALA A:139 , PHE A:142 , GLY A:197 , SER A:198 , PHE A:315 , MET A:331 , ARG A:335 , SER A:338 , TYR A:339 , THR A:342 , HIS A:343 , ARG A:346 , O A:551 , HOH A:903 , HOH A:908 , HOH A:956	BINDING SITE FOR RESIDUE HEM A 550
3	AC3	SOFTWARE	LEU B:42 , ASP B:46 , ARG B:53 , VAL B:54 , VAL B:55 , HIS B:56 , ARG B:93 , GLY B:112 , PHE B:113 , VAL B:127 , GLY B:128 , ASN B:129 , ALA B:139 , PHE B:142 , GLY B:197 , SER B:198 , HIS B:199 , PHE B:315 , MET B:331 , ARG B:335 , SER B:338 , TYR B:339 , THR B:342 , HIS B:343 , ARG B:346 , O B:551 , HOH B:558 , HOH B:581 , HOH B:618	BINDING SITE FOR RESIDUE HEM B 550
4	AC4	SOFTWARE	VAL A:55 , HIS A:56 , PHE A:142 , HEM A:550 , HOH A:1321	BINDING SITE FOR RESIDUE O A 551
5	AC5	SOFTWARE	HIS B:56 , PHE B:142 , HEM B:550 , HOH B:957	BINDING SITE FOR RESIDUE O B 551

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

Asymmetric Unit

No.	Residues
1	Thr A:384	-	Pro A:385
2	Met A:490	-	Lys A:491
3	Thr B:384	-	Pro B:385
4	Met B:490	-	Lys B:491

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

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_3	PS51402	catalase family profile.	CATA_HELPY	5-489	2	A:5-489 B:5-489
2	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_HELPY	45-61	2	A:45-61 B:45-61
3	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_HELPY	335-343	2	A:335-343 B:335-343

Biological Unit 1 (3, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CATALASE_3	PS51402	catalase family profile.	CATA_HELPY	5-489	4	A:5-489 B:5-489
2	CATALASE_2	PS00438	Catalase proximal active site signature.	CATA_HELPY	45-61	4	A:45-61 B:45-61
3	CATALASE_1	PS00437	Catalase proximal heme-ligand signature.	CATA_HELPY	335-343	4	A:335-343 B:335-343

(no "Exon" information available for 2IQF)

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:491
 aligned with CATA_HELPY | P77872 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:491
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
           CATA_HELPY     1 MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGERGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDAIKFPDFIHTQKRDPQTNLPNHDMVWDFWSNVPESLYQVTWVMSDRGIPKSFRHMDGFGSHTFSLINAKGERFWVKFHFHTMQGVKHLTNEEAAEVRKYDPDSNQRDLFNAIARGDFPKWKLSIQVMPEEDAKKYRFHPFDVTKIWYLQDYPLMEVGIVELNKNPENYFAEVEQAAFSPANVVPGIGYSPDRMLQGRLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYMQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRADDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMK 491
               SCOP domains d2iqfa_ A: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeee.hhh.....................eeeeeeeeee...hhhhhh.............ee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...................................hhhhh....hhhhh.........hhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CATALASE_3  PDB: A:5-489 UniProt: 5-489                                                                                                                                                                                                                                                                                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) --------------------------------------------CATALASE_2       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATALASE_---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iqf A   1 MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGERGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDAIKFPDFIHTQKRDPQTNLPNHDmVWDFWSNVPESLYQVTWVmSDRGIPKSFRHMDGFGSHTFSLINAKGERFWVKFHFHTMQGVKHLTNEEAAEIRKHDPDSNQRDLFDAIARGDYPKWKLSIQVMPEEDAKKYRFHPFDVTKIWYTQDYPLmEVGIVELNKNPENYFAEVEQAAFTPANVVPGIGYSPDRMLQGRLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYmQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRADDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMK 491
                                    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       310       320       330       340       350       360       370 |     380       390       400       410       420       430       440       450       460       470       480       490 
                                                                                                                                                                                           162-MHO            181-MHO                                                                                                        292-MHO                                                                         372-MHO

Chain B from PDB  Type:PROTEIN  Length:491
 aligned with CATA_HELPY | P77872 from UniProtKB/Swiss-Prot  Length:505

    Alignment length:491
                                    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       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490 
           CATA_HELPY     1 MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGERGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDAIKFPDFIHTQKRDPQTNLPNHDMVWDFWSNVPESLYQVTWVMSDRGIPKSFRHMDGFGSHTFSLINAKGERFWVKFHFHTMQGVKHLTNEEAAEVRKYDPDSNQRDLFNAIARGDFPKWKLSIQVMPEEDAKKYRFHPFDVTKIWYLQDYPLMEVGIVELNKNPENYFAEVEQAAFSPANVVPGIGYSPDRMLQGRLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYMQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRADDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMK 491
               SCOP domains d2iqfb_ B: Catalase I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................................hhhhhhhhhhhh............eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.ee....eeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeee.hhhhh...................eeeeeeeeee...hhhhhh.............ee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...................................hhhhh....hhhhh.........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----CATALASE_3  PDB: B:5-489 UniProt: 5-489                                                                                                                                                                                                                                                                                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) --------------------------------------------CATALASE_2       ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CATALASE_---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iqf B   1 MVNKDVKQTTAFGAPVWDDNNVITAGPRGPVLLQSTWFLEKLAAFDRERIPERVVHAKGSGAYGTFTVTKDITKYTKAKIFSKVGKKTECFFRFSTVAGERGSADAVRDPRGFAMKYYTEEGNWDLVGNNTPVFFIRDAIKFPDFIHTQKRDPQTNLPNHDmVWDFWSNVPESLYQVTWVmSDRGIPKSFRHMDGFGSHTFSLINAKGERFWVKFHFHTMQGVKHLTNEEAAEIRKHDPDSNQRDLFDAIARGDYPKWKLSIQVMPEEDAKKYRFHPFDVTKIWYTQDYPLmEVGIVELNKNPENYFAEVEQAAFTPANVVPGIGYSPDRMLQGRLFSYGDTHRYRLGVNYPQIPVNKPRCPFHSSSRDGYmQNGYYGSLQNYTPSSLPGYKEDKSARDPKFNLAHIEKEFEVWNWDYRADDSDYYTQPGDYYRSLPADEKERLHDTIGESLAHVTHKEIVDKQLEHFKKADPKYAEGVKKALEKHQKMMK 491
                                    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       310       320       330       340       350       360       370 |     380       390       400       410       420       430       440       450       460       470       480       490 
                                                                                                                                                                                           162-MHO            181-MHO                                                                                                        292-MHO                                                                         372-MHO

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)

Helicobacter pylori [TaxId: 210] (4)

1a	d2iqfa_	A:
1b	d2iqfb_	B:

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

(no "Pfam Domain" information available for 2IQF)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CATA_HELPY | P77872)

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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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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	Cis Peptide Bonds
		Met A:490 - Lys A:491	[ RasMol ]
		Met B:490 - Lys B:491	[ RasMol ]
		Thr A:384 - Pro A:385	[ RasMol ]
		Thr B:384 - Pro B:385	[ RasMol ]

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	2iqf
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	CATA_HELPY \| P77872
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UniProtKB/Swiss-Prot
	CATA_HELPY \| P77872	:	1qwl 1qwm 2a9e

1qwl	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI CATALASE
1qwm	CRYSTAL STRUCTURE OF HELICOBACTER PYLORI CATALASE WITH FORMIC ACID BOUND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

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