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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBOHYDRATE OXIDASE FROM MICRODOCHIUM NIVALE IN COMPLEX WITH SUBSTRATE ANALOGUE
 
Authors :  J. Duskova, T. Skalova, P. Kolenko, A. Stepankova, T. Koval, J. Hasek, L. H. Ostergaard, C. C. Fuglsang, J. Dohnalek
Date :  15 Apr 11  (Deposition) - 18 Apr 12  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein-Substrate Analogue Complex, Fad Binding Domain, Berberine And Berberine-Like Domain, Glucooligosaccharide Oxidase, Fad Binding, Carbohydrate/Sugar Binding, Extracellular, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Duskova, T. Skalova, P. Kolenko, A. Stepankova, J. Hasek, T. Koval, L. H. Ostergaard, C. C. Fuglsang, J. Dohnalek
Crystal Structure And Kinetic Studies Of Carbohydrate Oxidase From Microdochium Nivale
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOHYDRATE OXIDASE
    Chains: A
    EC Number: 1.1.3.4
    Engineered: YES
    Expression System: ASPERGILLUS ORYZAE
    Expression System Plasmid: PEJG33
    Expression System Strain: JAL228
    Expression System Taxid: 5062
    Expression System Vector Type: PLASMID
    Fragment: MATURE ENZYME
    Gene: MNCO
    Organism Scientific: MICRODOCHIUM NIVALE
    Organism Taxid: 5520
    Strain: NN008551

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 13)

Asymmetric/Biological Unit (7, 13)
No.NameCountTypeFull Name
1ABL2Ligand/Ion(2R,3R,4R,5R)-4,5-DIHYDROXY-2-(HYDROXYMETHYL)-6-OXOPIPERIDIN-3-YL BETA-D-GLUCOPYRANOSIDE
2CL4Ligand/IonCHLORIDE ION
3FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5SO41Ligand/IonSULFATE ION
6TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
7ZN3Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:29 , ALA A:65 , LYS A:66 , SER A:67 , GLY A:68 , GLY A:69 , HIS A:70 , SER A:71 , TYR A:72 , LEU A:88 , GLY A:130 , THR A:131 , CYS A:132 , VAL A:135 , GLY A:136 , SER A:138 , GLY A:139 , HIS A:140 , HIS A:143 , GLY A:145 , PHE A:146 , SER A:192 , GLY A:195 , ILE A:196 , VAL A:197 , GLN A:314 , TYR A:425 , ASN A:427 , TYR A:428 , ABL A:604 , HOH A:767 , HOH A:869 , HOH A:1144 , HOH A:1146 , HOH A:1148 , HOH A:1149 , HOH A:1151BINDING SITE FOR RESIDUE FAD A 501
02AC2SOFTWAREASN A:222 , SER A:225 , HOH A:722 , HOH A:975BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREHIS A:114 , ASP A:309 , HOH A:643 , HOH A:701BINDING SITE FOR RESIDUE ZN A 601
04AC4SOFTWAREASP A:306 , HIS A:307BINDING SITE FOR RESIDUE ZN A 602
05AC5SOFTWAREGLU A:231 , ASP A:235BINDING SITE FOR RESIDUE ZN A 603
06AC6SOFTWARETYR A:72 , ARG A:248 , TYR A:252 , ASN A:304 , GLN A:356 , GLN A:387 , TYR A:389 , ARG A:391 , TYR A:428 , FAD A:501 , HOH A:627 , HOH A:676 , HOH A:692 , HOH A:829 , HOH A:989 , HOH A:1095BINDING SITE FOR RESIDUE ABL A 604
07AC7SOFTWAREPRO A:13 , ILE A:14 , ASP A:15 , ILE A:16 , THR A:19 , ASP A:21 , TYR A:22 , GLN A:42 , CL A:608 , HOH A:682 , HOH A:753 , HOH A:915 , HOH A:1187BINDING SITE FOR RESIDUE ABL A 605
08AC8SOFTWAREGLN A:44 , ARG A:90 , MET A:91 , ILE A:92 , ASP A:93 , GLU A:107 , HOH A:710 , HOH A:1048BINDING SITE FOR RESIDUE TRS A 606
09AC9SOFTWAREALA A:9 , ARG A:32 , HOH A:651 , HOH A:735 , HOH A:1198BINDING SITE FOR RESIDUE SO4 A 607
10BC1SOFTWAREASP A:21 , ABL A:605BINDING SITE FOR RESIDUE CL A 608
11BC2SOFTWARELYS A:473BINDING SITE FOR RESIDUE CL A 609
12BC3SOFTWAREARG A:435 , TYR A:464 , CL A:611BINDING SITE FOR RESIDUE CL A 610
13BC4SOFTWAREARG A:435 , ARG A:470 , CL A:610BINDING SITE FOR RESIDUE CL A 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RJA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RJA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RJA)

(-) 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:473
 aligned with I1SB12_9PEZI | I1SB12 from UniProtKB/TrEMBL  Length:473

    Alignment length:473
                                    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   
         I1SB12_9PEZI     1 GAIEACLSAAGVPIDIPGTADYERDVEPFNIRLPYIPTAIAQTQTTAHIQSAVQCAKKLNLKVSAKSGGHSYASFGFGGENGHLMVQLDRMIDVISYNDKTGIAHVEPGARLGHLATVLNDKYGRAISHGTCPGVGISGHFAHGGFGFSSHMHGLAVDSVVGVTVVLADGRIVEASATENADLFWGIKGAGSNFGIVAVWKLATFPAPKVLTRFGVTLNWKNKTSALKGIEAVEDYARWVAPREVNFRIGDYGAGNPGIEGLYYGTPEQWRAAFQPLLDTLPAGYVVNPTTSLNWIESVLSYSNFDHVDFITPQPVENFYAKSLTLKSIKGDAVKNFVDYYFDVSNKVKDRFWFYQLDVHGGKNSQVTKVTNAETAYPHRDKLWLIQFYDRYDNNQTYPETSFKFLDGWVNSVTKALPKSDWGMYINYADPRMDRDYATKVYYGENLARLQKLKAKFDPTDRFYYPQAVRPVK 473
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh........hhhhhhhh............eeee..hhhhhhhhhhhhhhh...eeee.......hhhhh.....eeee......eeeee....eeee....hhhhhhhhhhhhhhee.........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeeee...hhhhhhhhhhhhhhh.eeeeeeee.ee....eeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee......eeeeeee.hhhhhhhhhhhhhh......ee...eeehhhhhhhhh...............eeeeeeeee....hhhhhhhhhhhhhhhhhh...eeeeeeee.....hhhhhh.............eeeeeeeee.........hhhhhhhhhhhhhhhhhhh.ee.hhhhh....hhhhhhhhhhh.hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rja A   1 GAIEACLSAAGVPIDIPGTADYERDVEPFNIRLPYIPTAIAQTQTTAHIQSAVQCAKKLNLKVSAKSGGHSYASFGFGGENGHLMVQLDRMIDVISYNDKTGIAHVEPGARLGHLATVLNDKYGRAISHGTCPGVGISGHFAHGGFGFSSHMHGLAVDSVVGVTVVLADGRIVEASATENADLFWGIKGAGSNFGIVAVWKLATFPAPKVLTRFGVTLNWKNKTSALKGIEAVEDYARWVAPREVNFRIGDYGAGNPGIEGLYYGTPEQWRAAFQPLLDTLPAGYVVNPTTSLNWIESVLSYSNFDHVDFITPQPVENFYAKSLTLKSIKGDAVKNFVDYYFDVSNKVKDRFWFYQLDVHGGKNSQVTKVTNAETAYPHRDKLWLIQFYDRYDNNQTYPETSFKFLDGWVNSVTKALPKSDWGMYINYADPRMDRDYATKVYYGENLARLQKLKAKFDPTDRFYYPQAVRPVK 473
                                    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
   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 3RJA)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RJA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (I1SB12_9PEZI | I1SB12)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0046562    glucose oxidase activity    Catalysis of the reaction: beta-D-glucose + O2 = D-glucono-1,5-lactone + H2O2.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    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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        I1SB12_9PEZI | I1SB12: 3rj8

(-) Related Entries Specified in the PDB File

3rj8