Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE, MUTANT C294A
 
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 :  1.77
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  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL5Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL4Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , GLY A:20 , PHE A:21 , ALA A:22 , HIS A:40 , GLU A:41 , LYS A:42 , 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 , TYR A:270 , GLY A:287 , ASP A:288 , PRO A:295 , ALA A:298 , GLY A:300 , ALA A:301 , GLY A:302 , HOH A:389 , HOH A:397 , HOH A:409 , HOH A:412 , HOH A:448 , HOH A:450 , HOH A:484 , HOH A:485BINDING SITE FOR RESIDUE FAD A 380
2AC2SOFTWARELEU A:179 , ARG A:211 , MET A:227 , PRO A:295 , HOH A:438BINDING SITE FOR RESIDUE GOL A 381
3AC3SOFTWAREGLY B:18 , GLY B:20 , PHE B:21 , ALA B:22 , HIS B:40 , GLU B:41 , LYS B:42 , ILE B:53 , TYR B:54 , ARG B:106 , SER B:128 , GLU B:129 , ALA B:130 , ALA B:155 , ASP B:156 , LEU B:179 , ARG B:181 , TYR B:270 , GLY B:287 , ASP B:288 , PRO B:295 , ALA B:298 , GLY B:300 , ALA B:301 , GLY B:302 , HOH B:397 , HOH B:403 , HOH B:411 , HOH B:428 , HOH B:431 , HOH B:449 , HOH B:486 , HOH B:495 , HOH B:523BINDING SITE FOR RESIDUE FAD B 380
4AC4SOFTWARELYS B:42 , GLU B:129 , GLN B:142 , HOH B:509BINDING SITE FOR RESIDUE GOL B 381
5AC5SOFTWAREGLU B:15 , ARG B:38 , HIS B:40 , SER B:125 , HOH B:507 , HOH B:549BINDING SITE FOR RESIDUE GOL B 382
6AC6SOFTWAREGLN B:74 , GLY B:75 , SER B:76 , ASN B:97 , PRO B:378 , HOH B:555BINDING SITE FOR RESIDUE GOL B 383
7AC7SOFTWARETRP B:173 , TYR B:270 , THR B:272 , ALA B:294 , GLY B:344 , ALA B:348BINDING SITE FOR RESIDUE GOL B 384

(-) SS Bonds  (0, 0)

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

(-) 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 3ALM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ALM)

(-) 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
                 3alm A  10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMAPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 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: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.....hhhhhh....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
                 3alm B  10 KTRRAEVAGGGFAGLTAAIALKQNGWDVRLHEKSSELRAFGAGIYLWHNGLRVLEGLGALDDVLQGSHTPPTYETWMHNKSVSKETFNGLPWRIMTRSHLHDALVNRARALGVDISVNSEAVAADPVGRLTLQTGEVLEADLIVGADGVGSKVRDSIGFKQDRWVSKDGLIRLIVPRMKKELGHGEWDNTIDMWNFWPRVQRILYSPCNENELYLGLMAPAADPRGSSVPIDLEVWVEMFPFLEPCLIEAAKLKTARYDKYETTKLDSWTRGKVALVGDAAHAMAPALAQGAGCAMVNAFSLSQDLEEGSSVEDALVAWETRIRPITDRCQALSGDYAANRSLSKGNMFTPAALEAARYDPLRRVYSWPQ 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
   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 3ALM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Trp A:206 - Pro A:207   [ RasMol ]  
    Trp B:206 - Pro B:207   [ RasMol ]  
    Val A:238 - Pro A:239   [ RasMol ]  
    Val B:238 - Pro B:239   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3alm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q988D3_RHILO | Q988D3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.14.12.4
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q988D3_RHILO | Q988D3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q988D3_RHILO | Q988D3: 3alj 3all 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
3all CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5- CARBOXYLIC ACID OXYGENASE, MUTANT Y270A