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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE, MUTANT Y270A
 
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 :  1.78
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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, B
    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
    Mutation: YES
    Organism Common: MESORHIZOBIUM LOTI
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 266835
    Strain: MAFF303099

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL5Ligand/IonGLYCEROL
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL3Ligand/IonGLYCEROL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY 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 , GLU A:129 , ALA A:130 , ALA A:155 , ASP A:156 , LEU A:179 , ARG A:181 , GLY A:287 , ASP A:288 , ALA A:298 , GLY A:300 , ALA A:301 , GLY A:302 , GOL A:384 , HOH A:387 , HOH A:406 , HOH A:408 , HOH A:411 , HOH A:426 , HOH A:428 , HOH A:531 , HOH A:546 , HOH A:594BINDING SITE FOR RESIDUE FAD A 380
2AC2SOFTWARETHR A:143 , SER A:175 , CYS A:294 , ALA A:347BINDING SITE FOR RESIDUE BME A 381
3AC3SOFTWAREGLN A:74 , GLY A:75 , SER A:76 , ASN A:218 , GLU A:219 , HOH A:578 , ASN B:97BINDING SITE FOR RESIDUE GOL A 382
4AC4SOFTWARESER A:277 , THR A:279 , ARG A:280 , GLY A:281 , HOH A:492BINDING SITE FOR RESIDUE GOL A 383
5AC5SOFTWARELEU A:179 , LEU A:213 , TYR A:223 , PRO A:295 , FAD A:380 , HOH A:490BINDING SITE FOR RESIDUE GOL A 384
6AC6SOFTWAREGLY B:18 , GLY B:20 , PHE B:21 , ALA B:22 , HIS B:40 , GLU B:41 , LYS B:42 , SER B:43 , ILE B:53 , TYR B:54 , ARG B:106 , SER B:128 , GLU B:129 , ALA B:130 , ALA B:155 , ASP B:156 , ARG B:181 , GLY B:287 , ASP B:288 , PRO B:295 , ALA B:298 , GLY B:300 , ALA B:301 , GLY B:302 , HOH B:403 , HOH B:408 , HOH B:410 , HOH B:420 , HOH B:428 , HOH B:434 , HOH B:448 , HOH B:455 , HOH B:497BINDING SITE FOR RESIDUE FAD B 380
7AC7SOFTWARESER B:175 , THR B:272 , CYS B:294BINDING SITE FOR RESIDUE BME B 381
8AC8SOFTWAREPRO A:378 , GLN A:379 , GLN B:74 , GLY B:75 , SER B:76 , HIS B:77BINDING SITE FOR RESIDUE GOL B 382
9AC9SOFTWARETHR B:11 , ARG B:12 , ASN B:33 , GLY B:34 , TRP B:35 , GLU B:316BINDING SITE FOR RESIDUE GOL B 383

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Trp A:206 -Pro A:207
2Val A:238 -Pro A:239
3Trp B:206 -Pro B:207
4Val B:238 -Pro B:239

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ALL)

(-) 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:370
 aligned with Q988D3_RHILO | Q988D3 from UniProtKB/TrEMBL  Length:379

    Alignment length:370
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379
         Q988D3_RHILO    10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 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..eeeee...eeeeeeee.hhhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhhh.....ee..eeeee...ee..eee.hhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3all A  10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKAETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with Q988D3_RHILO | Q988D3 from UniProtKB/TrEMBL  Length:379

    Alignment length:371
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378 
         Q988D3_RHILO     9 GKTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 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..eeeee..eeeeeeee..hhhhhh......eeeee.......eeeeeeee..eeeeeeeee...........hhhhhhhhh..hhhhhhhhhhh...eee..eeeee...ee..eee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3all B   9 GKTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKAETTKLDSWTRGKVALVGDAAHAMCPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 379
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
   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 3ALL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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: 3alj 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
3alj CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, REDUCED FORM
3alk CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT Y270F
3alm CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT C294A