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(-) Description

Title :  CRYSTAL STRUCTURE OF 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE
 
Authors :  K. M. Mcculloch, T. Mukherjee, T. P. Begley, S. E. Ealick
Date :  13 Mar 09  (Deposition) - 14 Apr 09  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Flavin Monooxygenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. M. Mcculloch, T. Mukherjee, T. P. Begley, S. E. Ealick
Structure Of The Plp Degradative Enzyme 2-Methyl-3-Hydroxypyridine-5-Carboxylic Acid Oxygenase From Mesorhizobium Loti Maff303099 And Its Mechanistic Implications.
Biochemistry V. 48 4139 2009
PubMed-ID: 19317437  |  Reference-DOI: 10.1021/BI900149F

(-) Compounds

Molecule 1 - 2-METHYL-3-HYDROXYPYRIDINE-5-CARBOXYLIC ACID OXYGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: XF1
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MLR6788
    Organism Common: MESORHIZOBIUM LOTI
    Organism Scientific: MESORHIZOBIUM LOTI
    Organism Taxid: 381

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE9Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 20)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , GLY A:19 , 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 , GLY A:157 , LEU A:179 , ARG A:181 , GLY A:287 , ASP A:288 , ALA A:298 , GLY A:300 , ALA A:301 , GLY A:302 , HOH A:380 , HOH A:422 , HOH A:424 , HOH A:425 , HOH A:448 , HOH A:467 , HOH A:495 , HOH A:496 , HOH A:534 , HOH A:578 , HOH A:624 , HOH A:628BINDING SITE FOR RESIDUE FAD A 400
2AC2SOFTWAREGLY B:18 , GLY B:19 , 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 , GLY B:157 , LEU B:179 , ARG B:181 , GLY B:287 , ASP B:288 , ALA B:298 , GLY B:300 , ALA B:301 , GLY B:302 , HOH B:384 , HOH B:394 , HOH B:398 , HOH B:412 , HOH B:421 , HOH B:475 , HOH B:547 , HOH B:642 , HOH B:649 , HOH B:688 , HOH B:692BINDING SITE FOR RESIDUE FAD B 400

(-) SS Bonds  (0, 0)

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

(-) 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 3GMB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3GMB)

(-) 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: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.eeeeehhhhhhhhhhhhhhhh.eee....eeeee...eeee....eee..eeee.....hhhhhh....eeeee...eeeeeeee.hhhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhh......ee..eeeee...ee..eee.hhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmb 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         
                                                                                                      86-MSE           104-MSE                                                                            187-MSE        202-MSE                  227-MSE              248-MSE                                      293-MSE     305-MSE                                             357-MSE                  


Chain B 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..eeeeee..........eeeeehhhhhhhhhh.hhhhhhh.......eeeee..eeeeeehhhhh.eeeeehhhhhhhhhhhhhhhh.eeee...eeeee...eeee....eee..eeee.....hhhhhhhh..eeeee...eeeeeeee.hhhhhh......eeeee.......eeeeee....eeeeeeee............hhhhhhhhh..hhhhhhhhh......ee..eeeee...ee..eee.hhhhhh......hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhee....ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gmb B  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         
                                                                                                      86-MSE           104-MSE                                                                            187-MSE        202-MSE                  227-MSE              248-MSE                                      293-MSE     305-MSE                                             357-MSE
   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 3GMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 3all 3alm 3gmc 4gf7 4h2n 4h2p 4h2q 4h2r 4jy2 4jy3 5hxi

(-) Related Entries Specified in the PDB File

3gmc CRYSTAL STRUCTURE OF SAME PROTEIN WITH SUBSTRATE BOUND