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(-) Description

Title :  HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASE 2
 
Authors :  A. Dong, H. Wu, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (S
Date :  14 Sep 10  (Deposition) - 27 Oct 10  (Release) - 27 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Serine Hydroxymethyltransferase 2, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wu, A. Dong, H. Zeng, P. Loppnau, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, A. N. Plotnikov, Structural Genomics Consortium (Sgc)
Crystal Structure Of Human Mitochondrial Serine Hydroxymethyltransferase 2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL
    ChainsA
    EC Number2.1.2.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneSHMT2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSHMT, SERINE METHYLASE, GLYCINE HYDROXYMETHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3OU5)

(-) Sites  (0, 0)

(no "Site" information available for 3OU5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OU5)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe A:304 -Pro A:305

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OU5)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYM_HUMAN272-288  1A:256-272
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYM_HUMAN272-288  1A:256-272
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SHMTPS00096 Serine hydroxymethyltransferase pyridoxal-phosphate attachment site.GLYM_HUMAN272-288  2A:256-272

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003289231bENSE00001325595chr12:57623552-5762359443GLYM_HUMAN1-11110--
1.3ENST000003289233ENSE00001594264chr12:57624586-57624783198GLYM_HUMAN12-77661A:26-6136
1.4ENST000003289234ENSE00001764231chr12:57625264-5762534380GLYM_HUMAN78-104271A:62-8322
1.5bENST000003289235bENSE00001738090chr12:57625496-57625696201GLYM_HUMAN104-171681A:94-149 (gaps)56
1.6ENST000003289236ENSE00001746009chr12:57625994-5762607582GLYM_HUMAN171-198281A:178-1825
1.7bENST000003289237bENSE00001294160chr12:57626236-57626358123GLYM_HUMAN199-239411A:183-22341
1.8ENST000003289238ENSE00001320599chr12:57626487-57626626140GLYM_HUMAN240-286471A:224-27047
1.9ENST000003289239ENSE00001303030chr12:57626963-57627128166GLYM_HUMAN286-341561A:270-325 (gaps)56
1.10ENST0000032892310ENSE00001318902chr12:57627346-57627445100GLYM_HUMAN342-375341A:326-35934
1.11ENST0000032892311ENSE00001301671chr12:57627532-57627687156GLYM_HUMAN375-427531A:359-41153
1.12ENST0000032892312ENSE00001328698chr12:57627786-57627893108GLYM_HUMAN427-463371A:411-44737
1.13bENST0000032892313bENSE00001317483chr12:57628017-57628714698GLYM_HUMAN463-504421A:447-48842

(-) 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:422
 aligned with GLYM_HUMAN | P34897 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:463
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501   
           GLYM_HUMAN    42 GWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH 504
               SCOP domains d3ou5a_ A: Serine hydroxymethyltransferase                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------SHMT-3ou5A01 A:33-432                                                                                                                                                                                                                                                                                                                                                                                           -------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhee........hhhhhhhhhhhhhh.....----------hhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhhh.-...ee...----------------------------...........hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhh.eeeee...hhhhhhh....hhhhh..eeeee..........eeeeee..eeee..--..eee..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..ee.hhh....eeeee.hhhh.hhhhhhhhhhhh.ee.eee............eeeeehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SHMT             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:26-61 [INCOMPLETE] Exon 1.4  PDB: A:62-83     ------------------------------------------------------------------Exon 1.6  PDB: A:178-182    Exon 1.7b  PDB: A:183-223                Exon 1.8  PDB: A:224-270 UniProt: 240-286      -------------------------------------------------------Exon 1.10  PDB: A:326-359         ---------------------------------------------------Exon 1.12  PDB: A:411-447            ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.5b  PDB: A:94-149 (gaps) UniProt: 104-171 [INCOMPLETE]       ------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:270-325 (gaps) UniProt: 286-341        ---------------------------------Exon 1.11  PDB: A:359-411 UniProt: 375-427           -----------------------------------Exon 1.13b  PDB: A:447-488                 Transcript 1 (2)
                 3ou5 A  26 GWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEG----------EVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQ-HDRIMGLD----------------------------PYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDP--GREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH 488
                                    35        45        55        65        75       | -        95       105       115       125       135    | |145   |     -         -         -  |    185       195       205       215       225       235       245       255       265       275       285  |    295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485   
                                                                                    83         94                                           140 |    149                          178                                                                                                        285  |                                                                                                                                                                                                        
                                                                                                                                              142                                                                                                                                               288                                                                                                                                                                                                        

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 2A7V: 2,2)

(no "CATH Domain" information available for 3OU5, only for superseded entry 2A7V replaced by 3OU5)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLYM_HUMAN | P34897)
molecular function
    GO:0008732    L-allo-threonine aldolase activity    Catalysis of the reaction: L-allo-threonine = glycine + acetaldehyde.
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0004372    glycine hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006564    L-serine biosynthetic process    The chemical reactions and pathways resulting in the formation of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    GO:0006563    L-serine metabolic process    The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
    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:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0019264    glycine biosynthetic process from serine    The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
    GO:0006544    glycine metabolic process    The chemical reactions and pathways involving glycine, aminoethanoic acid.
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0070536    protein K63-linked deubiquitination    A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0034340    response to type I interferon    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
    GO:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
cellular component
    GO:0070552    BRISC complex    A protein complex that contains the FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and MERIT40/NBA1 proteins, and specifically cleaves K63-linked polyubiquitin chains.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        GLYM_HUMAN | P348974pvf

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