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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN T-PROTEIN OF GLYCINE CLEAVAGE SYSTEM
 
Authors :  K. Okamura-Ikeda, H. Hosaka, M. Yoshimura, E. Yamashita, S. Toma, A. Nakagawa, K. Fujiwara, Y. Motokawa, H. Taniguchi
Date :  11 Nov 04  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glycine-Cleavage Sytem, Aminomethyl Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okamura-Ikeda, H. Hosaka, M. Yoshimura, E. Yamashita, S. Toma, A. Nakagawa, K. Fujiwara, Y. Motokawa, H. Taniguchi
Crystal Structure Of Human T-Protein Of Glycine Cleavage System At 2. 0A Resolution And Its Implication For Understanding Non-Ketotic Hyperglycinemia
J. Mol. Biol. V. 351 1146 2005
PubMed-ID: 16051266  |  Reference-DOI: 10.1016/J.JMB.2005.06.056
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - AMINOMETHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.2.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GCST
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GLYCINE CLEAVAGE SYSTEM T PROTEIN, GCVT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric/Biological Unit (2, 13)
No.NameCountTypeFull Name
1SO411Ligand/IonSULFATE ION
2THH2Ligand/IonN-[4-({[(6S)-2-AMINO-4-HYDROXY-5-METHYL-5,6,7,8-TETRAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC ACID

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:214 , HOH A:3167 , HOH A:3168 , ASP B:12 , VAL B:213 , HOH B:4011BINDING SITE FOR RESIDUE SO4 A 2001
02AC2SOFTWAREARG A:172 , HOH A:3201 , ARG B:290 , GLY B:317 , THR B:318 , TYR B:336BINDING SITE FOR RESIDUE SO4 A 2002
03AC3SOFTWAREHIS A:37 , ARG A:303 , HOH A:3137 , HOH A:3278 , HOH A:3370BINDING SITE FOR RESIDUE SO4 A 2003
04AC4SOFTWAREARG A:303 , ARG A:353 , HOH A:3250 , HOH A:3270BINDING SITE FOR RESIDUE SO4 A 2004
05AC5SOFTWAREHIS A:43 , LYS A:226 , LYS A:278BINDING SITE FOR RESIDUE SO4 A 2005
06AC6SOFTWAREARG A:287 , HOH A:3244BINDING SITE FOR RESIDUE SO4 A 2006
07AC7SOFTWARESER B:259 , LEU B:260 , SER B:261 , TRP B:262 , ARG B:291 , HOH B:4094BINDING SITE FOR RESIDUE SO4 B 2007
08AC8SOFTWARESER A:259 , LEU A:260 , SER A:261 , TRP A:262 , ARG A:291 , HOH A:3055 , HOH A:3252 , HOH A:3336BINDING SITE FOR RESIDUE SO4 A 2008
09AC9SOFTWAREARG B:303 , ARG B:353 , HOH B:4029BINDING SITE FOR RESIDUE SO4 B 2009
10BC1SOFTWAREHIS B:37 , ARG B:303 , PRO B:324 , HOH B:4004 , HOH B:4106BINDING SITE FOR RESIDUE SO4 B 2010
11BC2SOFTWAREHIS A:17 , ARG A:34 , ARG B:7 , HOH B:4160BINDING SITE FOR RESIDUE SO4 A 2011
12BC3SOFTWAREMET A:56 , LEU A:88 , ASP A:101 , LEU A:102 , ILE A:103 , VAL A:115 , ASN A:117 , PHE A:176 , MET A:177 , GLY A:196 , TYR A:197 , GLU A:204 , ARG A:233 , LEU A:242 , TRP A:262 , TYR A:371 , HOH A:3016 , HOH A:3025 , HOH A:3027 , HOH A:3198 , HOH A:3235BINDING SITE FOR RESIDUE THH A 3001
13BC4SOFTWAREMET B:56 , THR B:87 , LEU B:88 , ASP B:101 , ILE B:103 , VAL B:115 , ASN B:117 , PHE B:176 , MET B:177 , GLY B:196 , TYR B:197 , GLU B:204 , ARG B:233 , TRP B:262 , TYR B:371 , HOH B:4012 , HOH B:4050 , HOH B:4085 , HOH B:4099 , HOH B:4110 , HOH B:4193BINDING SITE FOR RESIDUE THH B 4001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WSV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Met A:364 -Pro A:365
2Met B:364 -Pro B:365

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 16)

Asymmetric/Biological Unit (8, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_007951H42RGCST_HUMANDisease (NKH)121964983A/BH14R
2UniProtVAR_007952G47RGCST_HUMANDisease (NKH)121964982A/BG19R
3UniProtVAR_016847N145IGCST_HUMANDisease (NKH)386833682A/BN117I
4UniProtVAR_016848E211KGCST_HUMANDisease (NKH)116192290A/BE183K
5UniProtVAR_074107R265CGCST_HUMANDisease (NKH)779483959A/BR237C
6UniProtVAR_007953G269DGCST_HUMANDisease (NKH)121964981A/BG241D
7UniProtVAR_007954D276HGCST_HUMANDisease (NKH)121964984A/BD248H
8UniProtVAR_007955R320HGCST_HUMANDisease (NKH)121964985A/BR292H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WSV)

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002735881aENSE00001875220chr3:49460186-49459794393GCST_HUMAN1-30300--
1.1mENST000002735881mENSE00001616814chr3:49459704-49459537168GCST_HUMAN31-86562A:4-58
B:4-58		55
55
1.1sENST000002735881sENSE00001754606chr3:49459005-4945892581GCST_HUMAN87-113272A:59-85
B:59-85		27
27
1.2cENST000002735882cENSE00001608529chr3:49457775-49457644132GCST_HUMAN114-157442A:86-129
B:86-129		44
44
1.2kENST000002735882kENSE00001775658chr3:49457221-4945714379GCST_HUMAN158-184272A:130-156
B:130-156		27
27
1.2oENST000002735882oENSE00001674578chr3:49456838-49456693146GCST_HUMAN184-232492A:156-204
B:156-204		49
49
1.2sENST000002735882sENSE00001676172chr3:49456584-49456404181GCST_HUMAN233-293612A:205-265
B:205-265		61
61
1.4bENST000002735884bENSE00001794841chr3:49455406-49455251156GCST_HUMAN293-345532A:265-317
B:265-317		53
53
1.5eENST000002735885eENSE00000968358chr3:49455151-49454212940GCST_HUMAN345-403592A:317-374
B:317-374		58
58

(-) 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:371
 aligned with GCST_HUMAN | P48728 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:371
                                    41        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 
           GCST_HUMAN    32 VLRRTPLYDFHLAHGGKMVAFAGWSLPVQYRDSHTDSHLHTRQHCSLFDVSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCPSPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTL 402
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wsvA01 A:4-55,A:147-240                            -------------------------------------------------------------------------------------------1wsvA01 A:4-55,A:147-240 Probable tRNA modification gtpase trme; domain 1                     ----------------------------------------------1wsvA04 A:287-363 Aminomethyltransferase beta-barrel domains                 ----------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh...eeee..eeee.....hhhhhhhhhhhheeeee....eeeeee..hhhhhhhh............eeeeeeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhhhhhhhh.....eeee...eeeeee..hhhhhhhh....hhhhh....eeeeee..eeeeeee........eeeeeehhhhhhhhhhhhhh...eee.hhhhhhhhhhhh...................hhhhhhhhhhhhh...hhhhhhhhhh....eeeeeeee.........eee.....eeeeeeeeeee....eeeeeeeee.hhh....eeeee....eeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------R----R-------------------------------------------------------------------------------------------------I-----------------------------------------------------------------K-----------------------------------------------------C---D------H-------------------------------------------H---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1m  PDB: A:4-58 UniProt: 31-86 [INCOMPLETE]     Exon 1.1s  PDB: A:59-85    Exon 1.2c  PDB: A:86-129 UniProt: 114-157   Exon 1.2k  PDB: A:130-156  ------------------------------------------------Exon 1.2s  PDB: A:205-265 UniProt: 233-293                   ---------------------------------------------------Exon 1.5e  PDB: A:317-374 UniProt: 345-403 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.2o  PDB: A:156-204 UniProt: 184-232       ------------------------------------------------------------Exon 1.4b  PDB: A:265-317 UniProt: 293-345           --------------------------------------------------------- Transcript 1 (2)
                 1wsv A   4 VLRRTPLYDFHLAHGGKMVAFAGWSLPVQYRDSHTDSHLHTRQHCSLFDVSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCPSPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTL 374
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373 


Chain B from PDB  Type:PROTEIN  Length:371
 aligned with GCST_HUMAN | P48728 from UniProtKB/Swiss-Prot  Length:403

    Alignment length:371
                                    41        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 
           GCST_HUMAN    32 VLRRTPLYDFHLAHGGKMVAFAGWSLPVQYRDSHTDSHLHTRQHCSLFDVSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCPSPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTL 402
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1wsvB01 B:4-55,B:147-240                            -------------------------------------------------------------------------------------------1wsvB01 B:4-55,B:147-240 Probable tRNA modification gtpase trme; domain 1                     ----------------------------------------------1wsvB04 B:287-363 Aminomethyltransferase beta-barrel domains                 ----------- CATH domains
           Pfam domains (1) ----------------------------------------------GCV_T-1wsvB01 B:50-263                                                                                                                                                                                                --------GCV_T_C-1wsvB03 B:272-364                                                                    ---------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------GCV_T-1wsvB02 B:50-263                                                                                                                                                                                                --------GCV_T_C-1wsvB04 B:272-364                                                                    ---------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhh...eeee..eeee.....hhhhhhhhhhhh.eeee....eeeeee..hhhhhhhh............eeeeeeee.....eeeeeeeee.....eeeee...hhhhhhhhhhhhhhhhhh.....eeee...eeeeee..hhhhhhhh....hhhhh....eeeeee..eeeeeee........eeeeeehhhhhhhhhhhhhh....ee.hhhhhhhhhhhh...................hhhhhhhhhhhhh...hhhhhhhhh......eeeeeee.........eee.....eeeeeeeeeee....eeeeeeeehhhhh....eeeeee..eeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------R----R-------------------------------------------------------------------------------------------------I-----------------------------------------------------------------K-----------------------------------------------------C---D------H-------------------------------------------H---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1m  PDB: B:4-58 UniProt: 31-86 [INCOMPLETE]     Exon 1.1s  PDB: B:59-85    Exon 1.2c  PDB: B:86-129 UniProt: 114-157   Exon 1.2k  PDB: B:130-156  ------------------------------------------------Exon 1.2s  PDB: B:205-265 UniProt: 233-293                   ---------------------------------------------------Exon 1.5e  PDB: B:317-374 UniProt: 345-403 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.2o  PDB: B:156-204 UniProt: 184-232       ------------------------------------------------------------Exon 1.4b  PDB: B:265-317 UniProt: 293-345           --------------------------------------------------------- Transcript 1 (2)
                 1wsv B   4 VLRRTPLYDFHLAHGGKMVAFAGWSLPVQYRDSHTDSHLHTRQHCSLFDVSHMLQTKILGSDRVKLMESLVVGDIAELRPNQGTLSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWEKDLALMQDKVRELQNQGRDVGLEVLDNALLALQGPTAAQVLQAGVADDLRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPVAGAVHLATAILKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRAAMDFPGAKVIVPQLKGRVQRRRVGLMCEGAPMRAHSPILNMEGTKIGTVTSGCPSPSLKKNVAMGYVPCEYSRPGTMLLVEVRRKQQMAVVSKMPFVPTNYYTL 374
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 1WSV)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: FBD (14)
(-)
Clan: no clan defined [family: GCV_T_C] (10)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GCST_HUMAN | P48728)
molecular function
    GO:0004047    aminomethyltransferase activity    Catalysis of the reaction: (6S)-tetrahydrofolate + S-aminomethyldihydrolipoylprotein = (6R)-5,10-methylenetetrahydrofolate + NH3 + dihydrolipoylprotein.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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:0006546    glycine catabolic process    The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid.
    GO:0019464    glycine decarboxylation via glycine cleavage system    The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
    GO:0046487    glyoxylate metabolic process    The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    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: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.

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  1wsv
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 Related Entries

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

UniProtKB/Swiss-Prot
        GCST_HUMAN | P48728: 1wsr

(-) Related Entries Specified in the PDB File

1wsr THE SAME PROTEIN