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(-) Description

Title :  X-RAY SIRAS STRUCTURE DETERMINATION OF A VANADIUM-DEPENDENT HALOPEROXIDASE FROM ASCOPHYLLUM NODOSUM AT 2.0 A RESOLUTION
 
Authors :  M. Weyand, H. -J. Hecht, M. Kiess, M. F. Liaud, H. Vilter, D. Schomburg
Date :  10 Jun 99  (Deposition) - 10 Jun 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bromoperoxidase, Vanadium, Haloperoxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Weyand, H. Hecht, M. Kiess, M. Liaud, H. Vilter, D. Schomburg
X-Ray Structure Determination Of A Vanadium-Dependent Haloperoxidase From Ascophyllum Nodosum At 2. 0 A Resolution.
J. Mol. Biol. V. 293 595 1999
PubMed-ID: 10543953  |  Reference-DOI: 10.1006/JMBI.1999.3179
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (VANADIUM BROMOPEROXIDASE)
    Chains: A, B
    EC Number: 1.11.1.10
    Organism Scientific: ASCOPHYLLUM NODOSUM
    Organism Taxid: 52969

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1IOD5Ligand/IonIODIDE ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3VO42Ligand/IonVANADATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:341 , ARG A:349 , PRO A:409 , HIS A:411 , SER A:416 , GLY A:417 , HIS A:418 , ARG A:480 , HIS A:486 , HOH A:1350BINDING SITE FOR RESIDUE VO4 A 600
2AC2SOFTWARELYS A:362 , TYR A:398BINDING SITE FOR RESIDUE IOD A 601
3AC3SOFTWAREMET A:153 , TYR A:447BINDING SITE FOR RESIDUE IOD A 602
4AC4SOFTWARETYR A:447 , ASP A:457 , PHE A:458 , HOH A:995BINDING SITE FOR RESIDUE IOD A 603
5AC5SOFTWARELYS B:341 , ARG B:349 , PRO B:409 , HIS B:411 , SER B:416 , GLY B:417 , HIS B:418 , ARG B:480 , HIS B:486 , HOH B:1387BINDING SITE FOR RESIDUE VO4 B 600
6AC6SOFTWAREMET B:153 , TYR B:447BINDING SITE FOR RESIDUE IOD B 601
7AC7SOFTWARETYR B:447 , ASP B:457 , HOH B:878BINDING SITE FOR RESIDUE IOD B 602

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:3 -B:41
2A:41 -B:3
3A:77 -A:86
4A:441 -A:462
5A:544 -A:555
6B:77 -B:86
7B:441 -B:462
8B:544 -B:555

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:414 -Pro A:415
2Tyr B:414 -Pro B:415

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QI9)

(-) Exons   (0, 0)

(no "Exon" information available for 1QI9)

(-) Sequences/Alignments

Asymmetric/Biological 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:555
 aligned with PRXV_ASCNO | P81701 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:555
                                    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     
           PRXV_ASCNO     2 TCSTSDDADDPTPPNERDDEAFASRVAAAKRELEGTGTVCQINNGETDLAAKFHKSLPHDDLGQVDADAFAALEDCILNGDLSICEDVPVGNSEGDPVGRLVNPTAAFAIDISGPAFSATTIPPVPTLPSPELAAQLAEVYWMALARDVPFMQYGTDDITVTAAANLAGMEGFPNLDAVSIGSDGTVDPLSQLFRATFVGVETGPFISQLLVNSFTIDSITVEPKQETFAPDVNYMVDFDEWLNIQNGGPPAGPELLDDELRFVRNARDLARVTFTDNINTEAYRGALILLGLDAFNRAGVNGPFIDIDRQAGFVNFGISHYFRLIGAAELAQRSSWYQKWQVHRFARPEALGGTLHLTIKGELNADFDLSLLENAELLKRVAAINAAQNPNNEVTYLLPQAIQEGSPTHPSYPSGHATQNGAFATVLKALIGLDRGGDCYPDPVYPDDDGLKLIDFRGSCLTFEGEINKLAVNVAFGRQMLGIHYRFDGIQGLLLGETITVRTLHQELMTFAEESTFEFRLFTGEVIKLFQDGTFTIDGFKCPGLVYTGVENCV 556
               SCOP domains d1qi9a_ A: Haloperoxidase (bromoperoxidase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1qi9A00 A:2-556 Vanadium-containing Chloroperoxidase, domain 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhh..hhhhh............................................hhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...................hhhh................hhhh..eee..eee................hhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhh..hhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhh.hhhh......eeeee....eeeee......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeee...eee..ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qi9 A   2 TCSTSDDADDPTPPNERDDEAFASRVAAAKRELEGTGTVCQINNGETDLAAKFHKSLPHDDLGQVDADAFAALEDCILNGDLSICEDVPVGNSEGDPVGRLVNPTAAFAIDISGPAFSATTIPPVPTLPSPELAAQLAEVYWMALARDVPFMQYGTDDITVTAAANLAGMEGFPNLDAVSIGSDGTVDPLSQLFRATFVGVETGPFISQLLVNSFTIDSITVEPKQETFAPDVNYMVDFDEWLNIQNGGPPAGPELLDDELRFVRNARDLARVTFTDNINTEAYRGALILLGLDAFNRAGVNGPFIDIDRQAGFVNFGISHYFRLIGAAELAQRSSWYQKWQVHRFARPEALGGTLHLTIKGELNADFDLSLLENAELLKRVAAINAAQNPNNEVTYLLPQAIQEGSPTHPSYPSGHATQNGAFATVLKALIGLDRGGDCYPDPVYPDDDGLKLIDFRGSCLTFEGEINKLAVNVAFGRQMLGIHYRFDGIQGLLLGETITVRTLHQELMTFAEESTFEFRLFTGEVIKLFQDGTFTIDGFKCPGLVYTGVENCV 556
                                    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     


Chain B from PDB  Type:PROTEIN  Length:556
 aligned with PRXV_ASCNO | P81701 from UniProtKB/Swiss-Prot  Length:557

    Alignment length:556
                                    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      
           PRXV_ASCNO     1 QTCSTSDDADDPTPPNERDDEAFASRVAAAKRELEGTGTVCQINNGETDLAAKFHKSLPHDDLGQVDADAFAALEDCILNGDLSICEDVPVGNSEGDPVGRLVNPTAAFAIDISGPAFSATTIPPVPTLPSPELAAQLAEVYWMALARDVPFMQYGTDDITVTAAANLAGMEGFPNLDAVSIGSDGTVDPLSQLFRATFVGVETGPFISQLLVNSFTIDSITVEPKQETFAPDVNYMVDFDEWLNIQNGGPPAGPELLDDELRFVRNARDLARVTFTDNINTEAYRGALILLGLDAFNRAGVNGPFIDIDRQAGFVNFGISHYFRLIGAAELAQRSSWYQKWQVHRFARPEALGGTLHLTIKGELNADFDLSLLENAELLKRVAAINAAQNPNNEVTYLLPQAIQEGSPTHPSYPSGHATQNGAFATVLKALIGLDRGGDCYPDPVYPDDDGLKLIDFRGSCLTFEGEINKLAVNVAFGRQMLGIHYRFDGIQGLLLGETITVRTLHQELMTFAEESTFEFRLFTGEVIKLFQDGTFTIDGFKCPGLVYTGVENCV 556
               SCOP domains d1qi9b_ B: Haloperoxidase (bromoperoxidase)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -1qi9B00 B:2-556 Vanadium-containing Chloroperoxidase, domain 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAP2-1qi9B01 B:318-514                                                                                                                                                                               ------------------------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PAP2-1qi9B02 B:318-514                                                                                                                                                                               ------------------------------------------ Pfam domains (2)
         Sec.struct. author ..............hhhhhhhhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhh..hhhhh............................................hhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...................hhhh................hhhh..eee..eee................hhhhhhhh....................hhhhhhhhhh....hhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh........hhhh..hhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhhhh.hhhh.......eee......eee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.....eeeee....eee..ee............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qi9 B   1 xTCSTSDDADDPTPPNERDDEAFASRVAAAKRELEGTGTVCQINNGETDLAAKFHKSLPHDDLGQVDADAFAALEDCILNGDLSICEDVPVGNSEGDPVGRLVNPTAAFAIDISGPAFSATTIPPVPTLPSPELAAQLAEVYWMALARDVPFMQYGTDDITVTAAANLAGMEGFPNLDAVSIGSDGTVDPLSQLFRATFVGVETGPFISQLLVNSFTIDSITVEPKQETFAPDVNYMVDFDEWLNIQNGGPPAGPELLDDELRFVRNARDLARVTFTDNINTEAYRGALILLGLDAFNRAGVNGPFIDIDRQAGFVNFGISHYFRLIGAAELAQRSSWYQKWQVHRFARPEALGGTLHLTIKGELNADFDLSLLENAELLKRVAAINAAQNPNNEVTYLLPQAIQEGSPTHPSYPSGHATQNGAFATVLKALIGLDRGGDCYPDPVYPDDDGLKLIDFRGSCLTFEGEINKLAVNVAFGRQMLGIHYRFDGIQGLLLGETITVRTLHQELMTFAEESTFEFRLFTGEVIKLFQDGTFTIDGFKCPGLVYTGVENCV 556
                            |       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      
                            1-PCA
   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/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: pap2 (9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PRXV_ASCNO | P81701)
molecular function
    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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 Related Entries

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