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(-) Description

Title :  CRYSTAL STRUCTURE OF HIGHLY GLYCOSYLATED PEROXIDASE FROM ROYAL PALM TREE
 
Authors :  L. Watanabe, P. R. Moura, L. Bleicher, A. S. Nascimento, L. S. Zamorano, J. J. Calvete, S. Bursakov, M. G. Roig, V. L. Shnyrov, I. Polikarpov
Date :  07 May 09  (Deposition) - 24 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Peroxidase, Palm Tree, Glycosylated, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Watanabe, P. R. De Moura, L. Bleicher, A. S. Nascimento, L. S. Zamorano, J. J. Calvete, L. Sanz, A. Perez, S. Bursakov, M. G. Roig V. L. Shnyrov, I. Polikarpov
Crystal Structure And Statistical Coupling Analysis Of Highly Glycosylated Peroxidase From Royal Palm Tree (Roystonea Regia).
J. Struct. Biol. V. 169 226 2010
PubMed-ID: 19854274  |  Reference-DOI: 10.1016/J.JSB.2009.10.009

(-) Compounds

Molecule 1 - ROYAL PALM TREE PEROXIDASE
    Chains: A
    EC Number: 1.11.1.-
    Organism Scientific: ROYSTONEA REGIA
    Organism Taxid: 145709

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (10, 58)

Asymmetric/Biological Unit (10, 58)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2EDO16Ligand/Ion1,2-ETHANEDIOL
3FUC5Ligand/IonALPHA-L-FUCOSE
4HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
5MAN8Ligand/IonALPHA-D-MANNOSE
6MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7NAG15Ligand/IonN-ACETYL-D-GLUCOSAMINE
8PEO1Ligand/IonHYDROGEN PEROXIDE
9SO48Ligand/IonSULFATE ION
10XYZ1Ligand/IonBETA-D-XYLOFURANOSE

(-) Sites  (58, 58)

Asymmetric Unit (58, 58)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:34 , ARG A:38 , PHE A:41 , SER A:73 , ARG A:75 , SER A:140 , PRO A:141 , LEU A:148 , PHE A:152 , LEU A:165 , SER A:166 , ALA A:168 , HIS A:169 , GLY A:172 , VAL A:173 , ALA A:174 , HIS A:175 , SER A:178 , LEU A:222 , LEU A:245 , SER A:247 , PEO A:309 , HOH A:592 , HOH A:593 , HOH A:714BINDING SITE FOR RESIDUE HEM A 305
02AC2SOFTWARESER A:170 , ASP A:223 , THR A:226 , VAL A:229 , ASP A:231BINDING SITE FOR RESIDUE CA A 306
03AC3SOFTWAREASP A:43 , VAL A:46 , GLY A:48 , ASP A:50 , SER A:52 , HOH A:594BINDING SITE FOR RESIDUE CA A 307
04AC4SOFTWAREARG A:38 , PHE A:41 , HIS A:42 , HEM A:305 , HOH A:376 , HOH A:587BINDING SITE FOR RESIDUE PEO A 309
05AC5SOFTWARESO4 A:312 , HOH A:435 , HOH A:436 , NAG A:500 , NAG A:501 , MAN A:504 , HOH A:607 , HOH A:837BINDING SITE FOR RESIDUE SO4 A 311
06AC6SOFTWAREARG A:75 , GLY A:76 , PHE A:77 , GLU A:78 , SO4 A:311 , EDO A:332 , MAN A:504 , HOH A:665 , HOH A:695BINDING SITE FOR RESIDUE SO4 A 312
07AC7SOFTWARENAG A:400 , NAG A:401 , MAN A:404 , HOH A:421BINDING SITE FOR RESIDUE SO4 A 313
08AC8SOFTWAREPRO A:198 , ILE A:225 , THR A:226 , PRO A:227 , SER A:228 , VAL A:229 , HOH A:310 , HOH A:625BINDING SITE FOR RESIDUE SO4 A 314
09AC9SOFTWARETYR A:117 , GLN A:118 , HOH A:445 , HOH A:735BINDING SITE FOR RESIDUE SO4 A 315
10BC1SOFTWARESER A:273 , HOH A:473 , HOH A:736 , NAG A:900 , NAG A:901BINDING SITE FOR RESIDUE SO4 A 316
11BC2SOFTWARENAG A:800 , NAG A:801 , HOH A:848 , HOH A:925BINDING SITE FOR RESIDUE SO4 A 317
12BC3SOFTWAREGLN A:93 , NAG A:600 , NAG A:601 , HOH A:811BINDING SITE FOR RESIDUE SO4 A 318
13BC4SOFTWARETHR A:13 , PRO A:141 , SER A:177 , THR A:213 , ARG A:214 , EDO A:329 , HOH A:590 , HOH A:591BINDING SITE FOR RESIDUE MES A 319
14BC5SOFTWARESER A:199 , LEU A:203 , VAL A:220 , SER A:221 , HOH A:368 , HOH A:516BINDING SITE FOR RESIDUE EDO A 320
15BC6SOFTWAREGLN A:277 , VAL A:280 , LYS A:281 , GLN A:284 , HOH A:483 , HOH A:692 , HOH A:713 , HOH A:864BINDING SITE FOR RESIDUE EDO A 321
16BC7SOFTWAREASN A:232 , ALA A:265 , MET A:266 , ASN A:267 , LEU A:268BINDING SITE FOR RESIDUE EDO A 322
17BC8SOFTWAREARG A:205 , HOH A:746BINDING SITE FOR RESIDUE EDO A 323
18BC9SOFTWARETHR A:9 , PRO A:12 , THR A:180 , TYR A:184 , ASN A:185 , HOH A:467 , HOH A:488 , HOH A:744BINDING SITE FOR RESIDUE EDO A 324
19CC1SOFTWAREARG A:47 , HOH A:828BINDING SITE FOR RESIDUE EDO A 326
20CC2SOFTWAREASN A:114 , LEU A:268 , ALA A:272 , EDO A:334 , HOH A:549 , HOH A:911BINDING SITE FOR RESIDUE EDO A 327
21CC3SOFTWARETHR A:62 , ASP A:66 , ASN A:135 , HOH A:441 , HOH A:835BINDING SITE FOR RESIDUE EDO A 328
22CC4SOFTWARESER A:16 , LEU A:17 , GLN A:20 , ARG A:214 , PHE A:215 , MES A:319 , HOH A:937BINDING SITE FOR RESIDUE EDO A 329
23CC5SOFTWARETYR A:184 , ASN A:185 , ARG A:205 , HOH A:496BINDING SITE FOR RESIDUE EDO A 330
24CC6SOFTWAREASN A:70 , ASN A:71 , PRO A:72 , LEU A:74 , PHE A:77 , HOH A:363 , MAN A:504 , HOH A:709 , HOH A:896BINDING SITE FOR RESIDUE EDO A 331
25CC7SOFTWARELYS A:65 , PHE A:77 , SO4 A:312 , MAN A:504 , HOH A:627 , HOH A:708 , HOH A:737BINDING SITE FOR RESIDUE EDO A 332
26CC8SOFTWAREGLY A:5 , TYR A:7 , CYS A:11 , PRO A:12 , GLU A:15BINDING SITE FOR RESIDUE EDO A 333
27CC9SOFTWAREILE A:115 , THR A:116 , ALA A:272 , SER A:273 , EDO A:327 , HOH A:339BINDING SITE FOR RESIDUE EDO A 334
28DC1SOFTWAREARG A:75 , ILE A:171 , GLY A:172 , PRO A:227 , SER A:228 , HOH A:661 , HOH A:923BINDING SITE FOR RESIDUE EDO A 335
29DC2SOFTWARETHR A:158 , ASP A:160 , HOH A:754 , HOH A:795 , HOH A:898BINDING SITE FOR RESIDUE EDO A 336
30DC3SOFTWAREILE A:4 , GLY A:5 , ASN A:8 , SO4 A:313 , NAG A:401 , FUC A:402 , HOH A:677 , HOH A:774 , HOH A:910BINDING SITE FOR RESIDUE NAG A 400
31DC4SOFTWAREGLN A:118 , SO4 A:313 , HOH A:360 , NAG A:400 , FUC A:402 , MAN A:403 , MAN A:404 , HOH A:677 , HOH A:774 , HOH A:867BINDING SITE FOR RESIDUE NAG A 401
32DC5SOFTWAREILE A:4 , HOH A:359 , NAG A:400 , NAG A:401 , HOH A:439 , HOH A:774 , HOH A:875BINDING SITE FOR RESIDUE FUC A 402
33DC6SOFTWARENAG A:401 , MAN A:404 , MAN A:405 , XYZ A:406 , HOH A:520BINDING SITE FOR RESIDUE MAN A 403
34DC7SOFTWARESO4 A:313 , NAG A:401 , MAN A:403 , HOH A:478BINDING SITE FOR RESIDUE MAN A 404
35DC8SOFTWAREMAN A:403 , HOH A:520BINDING SITE FOR RESIDUE MAN A 405
36DC9SOFTWAREMAN A:403 , HOH A:570BINDING SITE FOR RESIDUE XYZ A 406
37EC1SOFTWAREASN A:28 , ALA A:59 , SO4 A:311 , HOH A:347 , HOH A:379 , NAG A:501 , FUC A:502 , HOH A:734BINDING SITE FOR RESIDUE NAG A 500
38EC2SOFTWARESO4 A:311 , HOH A:349 , NAG A:500 , FUC A:502 , MAN A:503 , MAN A:504BINDING SITE FOR RESIDUE NAG A 501
39EC3SOFTWAREASN A:60 , NAG A:500 , NAG A:501BINDING SITE FOR RESIDUE FUC A 502
40EC4SOFTWAREHOH A:349 , NAG A:501 , MAN A:504 , HOH A:935BINDING SITE FOR RESIDUE MAN A 503
41EC5SOFTWAREPHE A:77 , SO4 A:311 , SO4 A:312 , EDO A:331 , EDO A:332 , HOH A:349 , HOH A:436 , HOH A:451 , HOH A:491 , NAG A:501 , MAN A:503 , HOH A:561 , HOH A:665 , HOH A:709BINDING SITE FOR RESIDUE MAN A 504
42EC6SOFTWAREASN A:144 , GLN A:147 , SO4 A:318 , HOH A:493 , NAG A:601 , FUC A:602 , HOH A:811BINDING SITE FOR RESIDUE NAG A 600
43EC7SOFTWARESO4 A:318 , HOH A:477 , NAG A:600 , FUC A:602BINDING SITE FOR RESIDUE NAG A 601
44EC8SOFTWAREHOH A:341 , HOH A:581 , NAG A:600 , NAG A:601BINDING SITE FOR RESIDUE FUC A 602
45EC9SOFTWAREASN A:154 , HOH A:308BINDING SITE FOR RESIDUE NAG A 700
46FC1SOFTWAREASN A:211 , SO4 A:317 , HOH A:389 , HOH A:697 , NAG A:801 , FUC A:802BINDING SITE FOR RESIDUE NAG A 800
47FC2SOFTWARESO4 A:317 , NAG A:800 , FUC A:802BINDING SITE FOR RESIDUE NAG A 801
48FC3SOFTWARENAG A:800 , NAG A:801BINDING SITE FOR RESIDUE FUC A 802
49FC4SOFTWAREASN A:267 , THR A:269 , ALA A:270 , SO4 A:316 , HOH A:408 , HOH A:460 , HOH A:533 , NAG A:901BINDING SITE FOR RESIDUE NAG A 900
50FC5SOFTWARESO4 A:316 , NAG A:900BINDING SITE FOR RESIDUE NAG A 901
51FC6SOFTWAREASP A:56 , ASN A:298 , SER A:300 , VAL A:301 , HOH A:380 , HOH A:722 , HOH A:752 , HOH A:902 , NAG A:1001 , FUC A:1002BINDING SITE FOR RESIDUE NAG A 1000
52FC7SOFTWAREASP A:56 , HOH A:380 , HOH A:562 , NAG A:1000 , FUC A:1002 , MAN A:1003 , MAN A:1004BINDING SITE FOR RESIDUE NAG A 1001
53FC8SOFTWAREHOH A:380 , HOH A:396 , NAG A:1000 , NAG A:1001BINDING SITE FOR RESIDUE FUC A 1002
54FC9SOFTWAREHOH A:527 , NAG A:1001 , MAN A:1004 , MAN A:1005BINDING SITE FOR RESIDUE MAN A 1003
55GC1SOFTWAREHOH A:348 , HOH A:391 , NAG A:1001 , MAN A:1003 , MAN A:1005BINDING SITE FOR RESIDUE MAN A 1004
56GC2SOFTWAREMAN A:1003 , MAN A:1004BINDING SITE FOR RESIDUE MAN A 1005
57GC3SOFTWAREASN A:114 , HOH A:497 , HOH A:508 , HOH A:532 , HOH A:554BINDING SITE FOR RESIDUE NAG A 1100
58GC4SOFTWAREASN A:256 , HOH A:495BINDING SITE FOR RESIDUE NAG A 1200

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:11 -A:91
2A:44 -A:49
3A:97 -A:299
4A:176 -A:208

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:71 -Pro A:72

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HDL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HDL)

(-) Exons   (0, 0)

(no "Exon" information available for 3HDL)

(-) 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:304
 aligned with D1MPT2_ROYRE | D1MPT2 from UniProtKB/TrEMBL  Length:304

    Alignment length:304
                                    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    
         D1MPT2_ROYRE     1 DLQIGFYNTSCPTAESLVQQAVAAAFANNSGIAPGLIRMHFHDCFVRGCDASVLLDSTANNTAEKDAIPNNPSLRGFEVITAAKSAVEAACPQTVSCADILAFAARDSANLAGNITYQVPSGRRDGTVSLASEANAQIPSPLFNATQLINSFANKTLTADEMVTLSGAHSIGVAHCSSFTNRLYNFNSGSGIDPTLSPSYAALLRNTCPANSTRFTPITVSLDIITPSVLDNMYYTGVQLTLGLLTSDQALVTEANLSAAVKANAMNLTAWASKFAQAMVKMGQIEVLTGTQGEIRTNCSVVNS 304
               SCOP domains d3hdla_ A: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3hdlA01 A:1-138,A:283-304  [code=1.10.520.10, no name defined]                                                                            3hdlA02 A:139-282 Peroxidase, domain 2                                                                                                          3hdlA01                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhh.......hhhhh........hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.....ee........hhhhhhhhh.....hhhhhhhhhhh...hhhhhhhhhhhhhh.eee.hhhhhhh.............hhhhhhhhhhhh..........eee..........hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hdl A   1 DLQIGFYNTSCPTAESLVQQAVAAAFANNSGIAPGLIRMHFHDCFVRGCDASVLLDSTANNTAEKDAIPNNPSLRGFEVITAAKSAVEAACPQTVSCADILAFAARDSANLAGNITYQVPSGRRDGTVSLASEANAQIPSPLFNATQLINSFANKTLTADEMVTLSGAHSIGVAHCSSFTNRLYNFNSGSGIDPTLSPSYAALLRNTCPANSTRFTPITVSLDIITPSVLDNMYYTGVQLTLGLLTSDQALVTEANLSAAVKANAMNLTAWASKFAQAMVKMGQIEVLTGTQGEIRTNCSVVNS 304
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HDL)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (D1MPT2_ROYRE | D1MPT2)
molecular function
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  3hdl
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 Related Entries

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