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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FAD-CONTAINING FNR-LIKE MODULE OF HUMAN METHIONINE SYNTHASE REDUCTASE
 
Authors :  K. R. Wolthers, X. Lou, H. S. Toogood, D. Leys, N. S. Scrutton
Date :  02 Aug 07  (Deposition) - 13 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha-Beta-Alpha Structural Motif, Flattened Antiparallel Beta Barrel, Flexible Hinge Region, Connecting Domain, Fad-Binding Region, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. R. Wolthers, X. Lou, H. S. Toogood, D. Leys, N. S. Scrutton
Mechanism Of Coenzyme Binding To Human Methionine Synthase Reductase Revealed Through The Crystal Structure Of The Fnr-Like Module And Isothermal Titration Calorimetry
Biochemistry V. 46 11833 2007
PubMed-ID: 17892308  |  Reference-DOI: 10.1021/BI701209P

(-) Compounds

Molecule 1 - METHIONINE SYNTHASE REDUCTASE
    ChainsA
    EC Number1.16.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4-T1
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentFNR-LIKE MODULE
    GeneMTRR
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMETHIONINE SYNTHASE REDUCTASE, MITOCHONDRIAL;
MSR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CSO3Mod. Amino AcidS-HYDROXYCYSTEINE
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECSO A:421 , ARG A:451 , PRO A:452 , TYR A:453 , SER A:454 , VAL A:469 , PHE A:470 , ASN A:471 , PHE A:475 , GLY A:487 , VAL A:488 , CYS A:489 , THR A:490 , ARG A:525 , TRP A:697 , HOH A:702 , HOH A:703 , HOH A:721 , HOH A:724 , HOH A:734 , HOH A:756 , HOH A:769 , HOH A:775 , HOH A:1050BINDING SITE FOR RESIDUE FAD A 700

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QTL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:233 -Pro A:234

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_034596S284TMTRR_HUMANPolymorphism2303080AS257T
2UniProtVAR_012840L360VMTRR_HUMANPolymorphism10064631AL333V
3UniProtVAR_034597K377RMTRR_HUMANPolymorphism162036AK350R
4UniProtVAR_012841C432RMTRR_HUMANDisease (HMAE)  ---AC405R
5UniProtVAR_034598R442CMTRR_HUMANPolymorphism2287780AR415C
6UniProtVAR_034599P477RMTRR_HUMANPolymorphism16879334AP450R
7UniProtVAR_012842G514RMTRR_HUMANDisease (HMAE)137853061AG487R
8UniProtVAR_015731G581RMTRR_HUMANDisease (HMAE)  ---AG554R
9UniProtVAR_014944H622YMTRR_HUMANPolymorphism10380AH595Y

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_FRPS51384 Ferredoxin reductase-type FAD binding domain profile.MTRR_HUMAN298-560  1A:272-533

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000002646685aENSE00000846013chr5:7869217-786930286MTRR_HUMAN1-19190--
1.9bENST000002646689bENSE00001701081chr5:7870883-7871036154MTRR_HUMAN19-70520--
1.11bENST0000026466811bENSE00000846011chr5:7873486-7873639154MTRR_HUMAN71-122520--
1.12cENST0000026466812cENSE00001702893chr5:7875371-7875488118MTRR_HUMAN122-161400--
1.13hENST0000026466813hENSE00001758099chr5:7878057-7878435379MTRR_HUMAN161-2871271A:217-25741
1.14bENST0000026466814bENSE00001631075chr5:7883268-7883390123MTRR_HUMAN288-328411A:272-30130
1.16aENST0000026466816aENSE00002154190chr5:7885814-7885967154MTRR_HUMAN329-380521A:302-35352
1.17bENST0000026466817bENSE00001695000chr5:7886728-788681689MTRR_HUMAN380-409301A:353-38230
1.18bENST0000026466818bENSE00000846005chr5:7889208-7889388181MTRR_HUMAN410-470611A:383-44361
1.20cENST0000026466820cENSE00000846004chr5:7891485-789152743MTRR_HUMAN470-484151A:443-45715
1.21bENST0000026466821bENSE00000846003chr5:7892840-7893026187MTRR_HUMAN484-546631A:457-519 (gaps)63
1.23ENST0000026466823ENSE00000846002chr5:7895847-7895965119MTRR_HUMAN547-586401A:520-55940
1.24bENST0000026466824bENSE00000846001chr5:7896977-789706993MTRR_HUMAN586-617321A:559-59032
1.25bENST0000026466825bENSE00000846000chr5:7897178-7897360183MTRR_HUMAN617-678621A:590-651 (gaps)62
1.26cENST0000026466826cENSE00001820245chr5:7900027-79012371211MTRR_HUMAN678-725481A:651-69848

(-) 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:448
 aligned with MTRR_HUMAN | Q9UBK8 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:482
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723  
           MTRR_HUMAN   244 SNVVIEDFESSLTRSVPPLSQASLNIPGLPPEYLQVHLQESLGQEESQVSVTSADPVFQVPISKAVQLTTNDAIKTTLLVELDISNTDFSYQPGDAFSVICPNSDSEVQSLLQRLQLEDKREHCVLLKIKADTKKKGATLPQHIPAGCSLQFIFTWCLEIRAIPKKAFLRALVDYTSDSAEKRRLQELCSKQGAADYSRFVRDACACLLDLLLAFPSCQPPLSLLLEHLPKLQPRPYSCASSSLFHPGKLHFVFNIVEFLSTATTEVLRKGVCTGWLALLVASVLQPNIHASHEDSGKALAPKISISPRTTNSFHLPDDPSIPIIMVGPGTGIAPFIGFLQHREKLQEQHPDGNFGAMWLFFGCRHKDRDYLFRKELRHFLKHGILTHLKVSFSRDAPVGEEEAPAKYVQDNIQLHGQQVARILLQENGHIYVCGDAKNMAKDVHDALVQIISKEVGVEKLEAMKTLATLKEEKRYLQDIWS 725
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------              FAD_binding_1-2qtlA01 A:272-492                                                                                                                                                                                              ---------              --------------------------NAD_binding_1-2qtlA02 A:542-662                                                                                          ------------------------------------ Pfam domains
         Sec.struct. author .................hhhhh...........eeeeee..--------------..eeeeeeeeee.........eeeeeee............eeeee...hhhhhhhhhhhh.hhhhh..eeeeee...................hhhhhhhhh.......hhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhh.....hhhhhhhhh.....hhhhhhhhh.....eeee..........eeeeeee..eee.......eeehhhhhhhhhhh....--------------...eeeeee...............eeee.hhhhhhhhhhhhhhhhhhhhhh.......eeeeeee........hhhhhhhhhhh....eeeeee.....------...hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------T---------------------------------------------------------------------------V----------------R------------------------------------------------------R---------C----------------------------------R------------------------------------R------------------------------------------------------------------R----------------------------------------Y------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------FAD_FR  PDB: A:272-533 UniProt: 298-560                                                                                                                                                                                                                                --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.13h  PDB: A:217-257 UniProt: 161-287 Exon 1.14b  PDB: A:272-301 [INCOMPLETE]  Exon 1.16a  PDB: A:302-353 UniProt: 329-380         -----------------------------Exon 1.18b  PDB: A:383-443 UniProt: 410-470                  -------------Exon 1.21b  PDB: A:457-519 (gaps) UniProt: 484-546             Exon 1.23  PDB: A:520-559               ------------------------------Exon 1.25b  PDB: A:590-651 (gaps) UniProt: 617-678            ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------------------------------------Exon 1.17b  PDB: A:353-382    ------------------------------------------------------------Exon 1.20c     -----------------------------------------------------------------------------------------------------Exon 1.24b  PDB: A:559-590      ------------------------------------------------------------Exon 1.26c  PDB: A:651-698 UniProt: 678-725      Transcript 1 (2)
                 2qtl A 217 SNVVIEDFESSLTRSVPPLSQASLNIPGLPPEYLQVHLQES--------------PVFQVPISKAVQLTTNDAIKTTLLVELDISNTDFSYQPGDAFSVICPNSDSEVQSLLQRLQLEDKREHcVLLKIKADTKKKGATLPQHIPAGcSLQFIFTWCLEIRAIPKKAFLRALVDYTSDSAEKRRLQELCSKQGAADYSRFVRDAcACLLDLLLAFPSCQPPLSLLLEHLPKLQPRPYSCASSSLFHPGKLHFVFNIVEFLSTATTEVLRKGVCTGWLALLVASVL--------------LAPKISIFPRTTNSFHLPDDPSIPIIMVGPGTGIAPFIGFLQHREKLQEQHPDGNFGAMWLFFGCRHKDRDYLFRKELRHFLKHGILTHLKVSFSRDAP------PAKYVQDNIQLHGQQVARILLQENGHIYVCGDAKNMAKDVHDALVQIISKEVGVEKLEAMKTLATLKEEKRYLQDIWS 698
                                   226       236       246       256|        -     | 276       286       296       306       316       326       336   |   346       356       366       376       386       396       406       416    |  426       436       446       456       466       476       486       496    |    -       516       526       536       546       556       566       576       586       596       606       | -    |  626       636       646       656       666       676       686       696  
                                                                  257            272                                                                 340-CSO                 364-CSO                                                  421-CSO                                                                         501            516                                                                                               614    621                                                                             

   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 2QTL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QTL)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MTRR_HUMAN | Q9UBK8)
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:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0003958    NADPH-hemoprotein reductase activity    Catalysis of the reaction: NADPH + H+ + n oxidized hemoprotein = NADP+ + n reduced hemoprotein.
    GO:0030586    [methionine synthase] reductase activity    Catalysis of the reaction: [methionine synthase]-cob(II)alamin + NADPH + H+ + S-adenosyl methionine = [methionine synthase]-methylcob(I)alamin + S-adenosylhomocysteine + NADP+.
    GO:0050444    aquacobalamin reductase (NADPH) activity    Catalysis of the reaction: 2 cob(II)alamin + NADP+ = 2 aquacob(III)alamin + NADPH + H+.
    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: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:0016723    oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered and NAD+ or NADP+ acts as an electron acceptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0033353    S-adenosylmethionine cycle    A cyclic series of interconversions involving S-adenosylmethionine, S-adenosyl-L-homocysteine, L-cysteine, and L-methionine. Couples utilization of the methyl group of SAM with recycling of the homocysteinyl group and regeneration of methionine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009235    cobalamin metabolic process    The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
    GO:0046655    folic acid metabolic process    The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0043418    homocysteine catabolic process    The chemical reactions and pathways resulting in the breakdown of homocysteine, the amino acid alpha-amino-gamma-mercaptobutanoic acid.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0006555    methionine metabolic process    The chemical reactions and pathways involving methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:1904042    negative regulation of cystathionine beta-synthase activity    Any process that stops, prevents or reduces the frequency, rate or extent of cystathionine beta-synthase activity.
    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.
    GO:0000096    sulfur amino acid metabolic process    The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0045111    intermediate filament cytoskeleton    Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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        MTRR_HUMAN | Q9UBK82qtz

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2qtz