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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE, REDUCED FORM
 
Authors :  J. Kobayashi, H. Yoshida, Y. Yoshikane, S. Kamitori, T. Yagi
Date :  04 Aug 10  (Deposition) - 10 Aug 11  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.48
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Kobayashi, H. Yoshida, Y. Yoshikane, S. Kamitori, T. Yagi
Crystal Structure Of 2-Methyl-3-Hydroxypyridine-5-Carboxyli Acid Oxygenase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE
    Chains: A
    EC Number: 1.14.12.4
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MLR6788
    Organism Common: MESORHIZOBIUM LOTI
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL7Ligand/IonGLYCEROL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:18 , GLY A:20 , PHE A:21 , ALA A:22 , HIS A:40 , GLU A:41 , LYS A:42 , SER A:43 , ILE A:53 , TYR A:54 , ARG A:106 , SER A:128 , GLU A:129 , ALA A:130 , ALA A:155 , ASP A:156 , LEU A:179 , ARG A:181 , GLY A:287 , ASP A:288 , PRO A:295 , ALA A:298 , GLY A:300 , ALA A:301 , GLY A:302 , HOH A:390 , HOH A:394 , HOH A:402 , HOH A:405 , HOH A:408 , HOH A:431 , HOH A:439 , HOH A:506 , HOH A:513 , HOH A:535 , HOH A:570 , HOH A:583 , HOH A:617BINDING SITE FOR RESIDUE FAD A 380
02AC2SOFTWAREGLN A:142 , TYR A:270 , CYS A:294 , ALA A:347 , GOL A:386 , HOH A:529BINDING SITE FOR RESIDUE BME A 381
03AC3SOFTWAREASN A:58 , CYS A:303 , VAL A:306 , ILE A:335 , THR A:336 , ALA A:365 , TYR A:368BINDING SITE FOR RESIDUE BME A 382
04AC4SOFTWARELYS A:169 , GLN A:170 , ASP A:171 , LYS A:274 , ASP A:276 , HOH A:443BINDING SITE FOR RESIDUE GOL A 383
05AC5SOFTWARELYS A:42 , GLU A:129 , LYS A:161 , LYS A:274 , GLN A:340 , HOH A:443 , HOH A:470 , HOH A:499 , HOH A:540 , HOH A:542BINDING SITE FOR RESIDUE GOL A 384
06AC6SOFTWARETRP A:85 , ASN A:88 , LYS A:89 , PHE A:251 , HOH A:543BINDING SITE FOR RESIDUE GOL A 385
07AC7SOFTWAREARG A:211 , TYR A:270 , CYS A:294 , PRO A:295 , ALA A:296 , ALA A:347 , BME A:381 , HOH A:432 , HOH A:474 , HOH A:525 , HOH A:590 , HOH A:623BINDING SITE FOR RESIDUE GOL A 386
08AC8SOFTWAREGLN A:74 , GLY A:75 , SER A:76 , ASN A:97 , GLU A:219 , HOH A:666BINDING SITE FOR RESIDUE GOL A 387
09AC9SOFTWAREHIS A:57 , LEU A:60 , ARG A:61 , GLU A:64 , HOH A:603BINDING SITE FOR RESIDUE GOL A 388
10BC1SOFTWAREGLU A:364 , ARG A:367 , TYR A:375BINDING SITE FOR RESIDUE GOL A 389

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:206 -Pro A:207
2Val A:238 -Pro A:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ALJ)

(-) 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:369
 aligned with Q988D3_RHILO | Q988D3 from UniProtKB/TrEMBL  Length:379

    Alignment length:369
                                    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         
         Q988D3_RHILO    11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh..eeeee...........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhh..eee....eeeee...eeee....eee..eeee.....hhhhhhhh..eeeeeeeeeeeeeeee.hhhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhhh.....eeeeeeeee...ee..eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3alj A  11 TRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    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
   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 3ALJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q988D3_RHILO | Q988D3)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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.
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

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

UniProtKB/TrEMBL
        Q988D3_RHILO | Q988D3: 3all 3alm 3gmb 3gmc 4gf7 4h2n 4h2p 4h2q 4h2r 4jy2 4jy3 5hxi

(-) Related Entries Specified in the PDB File

3alh CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, FREE FORM
3ali CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, 5-PYRIDOXIC ACID BOUND FORM
3alk CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT Y270F
3all CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT Y270A
3alm CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT C294A