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(-) Description

Title :  PVC-AT
 
Authors :  A. Borovik, W. R. Melik-Adamyan
Date :  20 May 10  (Deposition) - 16 Jun 10  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,E
Biol. Unit 1:  A,E  (2x)
Keywords :  Oxidoreductase, Metal-Binding, Peroxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Borovik, A. I. Grebenko, W. R. Melik-Adamyan
X-Ray Investigation Of Penicillium Vitale Catalase Inhibited By Aminotriazole
Crystallography Reports V. 56 590 2011
PubMed: search  |  Reference-DOI: 10.1134/S1063774511030060

(-) Compounds

Molecule 1 - CATALASE
    Chains: A, E
    EC Number: 1.11.1.6
    Organism Scientific: PENICILLIUM JANTHINELLUM
    Organism Taxid: 5079

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AE
Biological Unit 1 (2x): AE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
13TR2Ligand/Ion3-AMINO-1,2,4-TRIAZOLE
2CA6Ligand/IonCALCIUM ION
3HDD2Ligand/IonCIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 20)
No.NameCountTypeFull Name
13TR4Ligand/Ion3-AMINO-1,2,4-TRIAZOLE
2CA-1Ligand/IonCALCIUM ION
3HDD4Ligand/IonCIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE
4NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:61 , VAL A:63 , HIS A:64 , ARG A:101 , GLY A:120 , VAL A:135 , GLY A:136 , ASN A:137 , PHE A:150 , VAL A:210 , HIS A:211 , PHE A:327 , LEU A:343 , ARG A:347 , SER A:350 , TYR A:351 , THR A:354 , GLN A:355 , ARG A:358 , 3TR A:695 , HOH A:2477 , HOH A:2478BINDING SITE FOR RESIDUE HDD A 690
02AC2SOFTWAREASN A:410 , THR A:412 , VAL A:413BINDING SITE FOR RESIDUE NAG A 691
03AC3SOFTWAREHIS A:511 , ASP A:512 , ASN A:513 , HOH A:2479 , HOH A:2480 , SER E:87 , ASP E:128 , GLU E:129 , LYS E:415BINDING SITE FOR RESIDUE NAG A 692
04AC4SOFTWAREASP A:79 , ASN A:82BINDING SITE FOR RESIDUE NAG A 693
05AC5SOFTWAREHIS A:64 , VAL A:105 , ASN A:137 , PHE A:142 , PHE A:150 , HDD A:690BINDING SITE FOR RESIDUE 3TR A 695
06AC6SOFTWAREARG E:61 , VAL E:63 , HIS E:64 , ARG E:101 , GLY E:120 , VAL E:135 , GLY E:136 , ASN E:137 , PHE E:150 , VAL E:210 , HIS E:211 , PHE E:327 , LEU E:343 , ARG E:347 , SER E:350 , TYR E:351 , THR E:354 , GLN E:355 , ARG E:358 , 3TR E:695 , HOH E:2420 , HOH E:2421BINDING SITE FOR RESIDUE HDD E 690
07AC7SOFTWAREASN E:410 , THR E:412 , VAL E:413 , HOH E:2422BINDING SITE FOR RESIDUE NAG E 691
08AC8SOFTWAREASN E:513BINDING SITE FOR RESIDUE NAG E 692
09AC9SOFTWAREASP E:79 , SER E:81 , ASN E:82BINDING SITE FOR RESIDUE NAG E 693
10BC1SOFTWAREHIS E:64 , VAL E:105 , ASN E:137 , PHE E:142 , PHE E:150 , HDD E:690BINDING SITE FOR RESIDUE 3TR E 695
11BC2SOFTWAREGLU A:95 , SER A:653 , GLU A:654 , ARG A:655 , VAL A:658 , HOH A:2451BINDING SITE FOR RESIDUE CA A1690
12BC3SOFTWARESER E:653 , ARG E:655 , VAL E:658BINDING SITE FOR RESIDUE CA E1690
13BC4SOFTWAREHOH A:2194 , HOH A:2440 , HOH A:2441 , HOH A:2443 , HOH E:2181 , HOH E:2182 , HOH E:2400 , HOH E:2402BINDING SITE FOR RESIDUE CA A1691
14BC5SOFTWAREHOH A:2109 , HOH A:2274 , HOH A:2276 , HOH E:2257BINDING SITE FOR RESIDUE CA E1692
15BC6SOFTWARETHR A:432 , HOH A:2127 , HOH A:2128 , HOH A:2342 , HOH E:2029 , HOH E:2031 , HOH E:2034BINDING SITE FOR RESIDUE CA A1692
16BC7SOFTWAREHOH A:2035 , HOH A:2038 , HOH A:2040 , THR E:432 , HOH E:2122 , HOH E:2123 , HOH E:2319BINDING SITE FOR RESIDUE CA E1691

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XF2)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ile A:165 -Pro A:166
2Ser A:397 -Pro A:398
3Ser A:405 -Pro A:406
4Ile E:165 -Pro E:166
5Ser E:397 -Pro E:398
6Ser E:405 -Pro E:406

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XF2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2XF2)

(-) Exons   (0, 0)

(no "Exon" information available for 2XF2)

(-) 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:688
 aligned with D9N167_PENJA | D9N167 from UniProtKB/TrEMBL  Length:688

    Alignment length:688
                                    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       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680        
         D9N167_PENJA     1 QQFLSQFYLNDQDVYLTSNVGGPIQDENSLSAGQRGATLLQDFIFREKIQRFDHERVPERAVHARGTGAHGTFTSYGDWSNLTAASFLSAEGKETPMFTRFSTVAGSRGSADTARDVHGFATRFYTDEGNFDIVGNNIPVFFIQDAILFPDLIHAVKPRGDNQIPQAATAHDSAWDFFSQQPSVLHTLLWAMAGHGIPRSFRHVNGFGVHTFRLVTDDGKTKLVKFHWKGLQGKASFVWEEAQQTAGKNADFMRQDLFQSIQAGRFPEWELGVQIMQEQDQLKFGFDLLDPTKIVPEELVPVTILGKMQLNRNPMNYFAETEQVMFQPGHIVRGVDFTEDPLLQGRLFSYLDTQLNRHGGPNFEQLPINRPRAPIHNNNRDGAGQMFIPLDPNAYSPNTENKGSPKQANETVGKGFFTAPERTASGKLQRTLSTTFENNWSQPRLFWNSLVNAQKEFIVDAMRFETSNVSSSVVRDDVIIQLNRISDNLATRVASAIGVEAPKPNSSFYHDNTTAHIGAFGEKLAKLDGLKVGLLASVNKPASIAQGAKLQVALSSVGVDVVVVAERMANNVDETYSASDAVQFDAVVVADGAEGLFGADSFTVEPSAGSGASTLYPAGRPLNILLDAFRFGKTVGALGSGSDALESGQISSERQGVYTGKNAGDAFAKDIKSGLSTFKFLDRFAVDE 688
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......................ee.........hhhhhhhhhhhhh...........eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.ee.............eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeehhhhh....................eeeeeeeeeee...hhhhhh..................hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........................................................ee...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.....................eeeee....hhhhhhhhhhhhhhhhhhh.eeeeee........ee.hhhhhhhh.eeee...hhhhhh........hhhhh.......hhhhhhhhhhhhhh.eeeee..hhhhhhhh........eeee...hhhhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xf2 A   2 QQFLSQFYLNDQDVYLTSNVGGPIQDENSLSAGQRGATLLQDFIFREKIQRFDHERVPERAVHARGTGAHGTFTSYGDWSNLTAASFLSAEGKETPMFTRFSTVAGSRGSADTARDVHGFATRFYTDEGNFDIVGNNIPVFFIQDAILFPDLIHAVKPRGDNQIPQAATAHDSAWDFFSQQPSVLHTLLWAMAGHGIPRSFRHVNGFGVHTFRLVTDDGKTKLVKFHWKGLQGKASFVWEEAQQTAGKNADFMRQDLFQSIQAGRFPEWELGVQIMQEQDQLKFGFDLLDPTKIVPEELVPVTILGKMQLNRNPMNYFAETEQVMFQPGHIVRGVDFTEDPLLQGRLFSYLDTQLNRHGGPNFEQLPINRPRAPIHNNNRDGAGQMFIPLDPNAYSPNTENKGSPKQANETVGKGFFTAPERTASGKLQRTLSTTFENNWSQPRLFWNSLVNAQKEFIVDAMRFETSNVSSSVVRDDVIIQLNRISDNLATRVASAIGVEAPKPNSSFYHDNTTAHIGAFGEKLAKLDGLKVGLLASVNKPASIAQGAKLQVALSSVGVDVVVVAERMANNVDETYSASDAVQFDAVVVADGAEGLFGADSFTVEPSAGSGASTLYPAGRPLNILLDAFRFGKTVGALGSGSDALESGQISSERQGVYTGKNAGDAFAKDIKSGLSTFKFLDRFAVDE 689
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681        


Chain E from PDB  Type:PROTEIN  Length:688
 aligned with D9N167_PENJA | D9N167 from UniProtKB/TrEMBL  Length:688

    Alignment length:688
                                    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       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680        
         D9N167_PENJA     1 QQFLSQFYLNDQDVYLTSNVGGPIQDENSLSAGQRGATLLQDFIFREKIQRFDHERVPERAVHARGTGAHGTFTSYGDWSNLTAASFLSAEGKETPMFTRFSTVAGSRGSADTARDVHGFATRFYTDEGNFDIVGNNIPVFFIQDAILFPDLIHAVKPRGDNQIPQAATAHDSAWDFFSQQPSVLHTLLWAMAGHGIPRSFRHVNGFGVHTFRLVTDDGKTKLVKFHWKGLQGKASFVWEEAQQTAGKNADFMRQDLFQSIQAGRFPEWELGVQIMQEQDQLKFGFDLLDPTKIVPEELVPVTILGKMQLNRNPMNYFAETEQVMFQPGHIVRGVDFTEDPLLQGRLFSYLDTQLNRHGGPNFEQLPINRPRAPIHNNNRDGAGQMFIPLDPNAYSPNTENKGSPKQANETVGKGFFTAPERTASGKLQRTLSTTFENNWSQPRLFWNSLVNAQKEFIVDAMRFETSNVSSSVVRDDVIIQLNRISDNLATRVASAIGVEAPKPNSSFYHDNTTAHIGAFGEKLAKLDGLKVGLLASVNKPASIAQGAKLQVALSSVGVDVVVVAERMANNVDETYSASDAVQFDAVVVADGAEGLFGADSFTVEPSAGSGASTLYPAGRPLNILLDAFRFGKTVGALGSGSDALESGQISSERQGVYTGKNAGDAFAKDIKSGLSTFKFLDRFAVDE 688
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh......................ee.........hhhhhhhhhhhhh...........eeeeeeeeee.........hhhhh....eeeeeeeee................eeeeeeee..eeeeeeee........hhhhhhhhhhhhh.............hhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhh.eeeeeeeeee.....eeeeeeeeee.......hhhhhhhhhhhh.hhhhhhhhhhhhh....eeeeeeeeehhhhh....................eeeeeeeeeee...hhhhhh.............ee...hhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.........................................................ee...hhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhh.....................eeeee....hhhhhhhhhhhhhhhhhhh.eeeeee........ee....hhhhh.eeee...hhhhhh........hhhhh.......hhhhhhhhhhhhhh.eeeee..hhhhhhhh........eeee...hhhhhhhhhhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xf2 E   2 QQFLSQFYLNDQDVYLTSNVGGPIQDENSLSAGQRGATLLQDFIFREKIQRFDHERVPERAVHARGTGAHGTFTSYGDWSNLTAASFLSAEGKETPMFTRFSTVAGSRGSADTARDVHGFATRFYTDEGNFDIVGNNIPVFFIQDAILFPDLIHAVKPRGDNQIPQAATAHDSAWDFFSQQPSVLHTLLWAMAGHGIPRSFRHVNGFGVHTFRLVTDDGKTKLVKFHWKGLQGKASFVWEEAQQTAGKNADFMRQDLFQSIQAGRFPEWELGVQIMQEQDQLKFGFDLLDPTKIVPEELVPVTILGKMQLNRNPMNYFAETEQVMFQPGHIVRGVDFTEDPLLQGRLFSYLDTQLNRHGGPNFEQLPINRPRAPIHNNNRDGAGQMFIPLDPNAYSPNTENKGSPKQANETVGKGFFTAPERTASGKLQRTLSTTFENNWSQPRLFWNSLVNAQKEFIVDAMRFETSNVSSSVVRDDVIIQLNRISDNLATRVASAIGVEAPKPNSSFYHDNTTAHIGAFGEKLAKLDGLKVGLLASVNKPASIAQGAKLQVALSSVGVDVVVVAERMANNVDETYSASDAVQFDAVVVADGAEGLFGADSFTVEPSAGSGASTLYPAGRPLNILLDAFRFGKTVGALGSGSDALESGQISSERQGVYTGKNAGDAFAKDIKSGLSTFKFLDRFAVDE 689
                                    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       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681
   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  (0, 0)

(no "SCOP Domain" information available for 2XF2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XF2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XF2)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,E   (D9N167_PENJA | D9N167)
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.

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  2xf2
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  D9N167_PENJA | D9N167
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 Related Entries

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

UniProtKB/TrEMBL
        D9N167_PENJA | D9N167: 2iuf

(-) Related Entries Specified in the PDB File

2iuf THE STRUCTURES OF PENICILLIUM VITALE CATALASE: RESTING STATE, OXIDISED STATE (COMPOUND I) AND COMPLEX WITH AMINOTRIAZOLE