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(-) Description

Title :  THE CRYSTAL STRUCTURE OF Y334C MUTANT OF HUMAN SEPSECS IN COMPLEX WITH SELENOCYSTEINE TRNA (TRNASEC)
 
Authors :  R. L. French, M. Simonovic
Date :  17 Apr 15  (Deposition) - 20 Apr 16  (Release) - 05 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A (2x),B (2x),E (1x)
Biol. Unit 2:  C (2x),D (2x),E (1x)
Keywords :  Selenocysteine, Trna, Mutation, Pyridoxal Phosphate, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Puppala, R. L. French, D. Matthies, U. Baxa, S. Subramaniam, M. Simonovic
Structural Basis For Early-Onset Neurological Disorders Caused By Mutations In Human Selenocysteine Synthase.
Sci Rep V. 6 32563 2016
PubMed-ID: 27576344  |  Reference-DOI: 10.1038/SREP32563

(-) Compounds

Molecule 1 - O-PHOSPHOSERYL-TRNA(SEC) SELENIUM TRANSFERASE
    Chains: A, B, C, D
    EC Number: 2.9.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE80
    Expression System Strain: SOLUBL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SEPSECS, TRNP48
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SELENOCYSTEINE TRNA
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (2x): A (2x)B (2x)  E (1x)
Biological Unit 2 (2x):   C (2x)D (2x)E (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1PLR4Ligand/Ion(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1PLR4Ligand/Ion(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE
2PO44Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1PLR4Ligand/Ion(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGENPHOSPHATE
2PO44Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:75 , ALA A:143 , THR A:144 , GLY A:145 , ILE A:170 , GLN A:172 , SER A:174 , CYS A:175 , ASN A:252 , ALA A:254 , TYR A:255 , LYS A:284 , GLY A:312 , ARG A:313 , HOH A:1108binding site for residue PLR A 1001
2AC2SOFTWAREARG A:97 , GLN A:105 , HOH A:1163binding site for residue PO4 A 1002
3AC3SOFTWAREARG B:75 , SER B:98 , ALA B:143 , THR B:144 , GLY B:145 , ILE B:170 , GLN B:172 , SER B:174 , ASN B:252 , TYR B:255 , LYS B:284 , GLY B:312 , ARG B:313 , HOH B:1175binding site for residue PLR B 1001
4AC4SOFTWAREARG B:97 , GLN B:105 , ARG B:313 , HOH B:1136binding site for residue PO4 B 1002
5AC5SOFTWAREARG C:97 , GLN C:105 , ARG C:313 , HOH C:1148binding site for residue PO4 C 1002
6AC6SOFTWAREARG D:97 , SER D:98 , GLN D:105 , ARG D:313 , HOH D:1105 , HOH D:1108 , HOH D:1125binding site for residue PO4 D 1002
7AC7SOFTWAREARG C:75 , ALA C:143 , THR C:144 , GLY C:145 , ILE C:170 , GLN C:172 , SER C:174 , CYS C:175 , ASN C:252 , ALA C:254 , TYR C:255 , SER C:281 , LEU C:282 , ASP C:283 , ASN C:285 , GLY C:312 , ARG C:313 , HOH C:1102 , HOH C:1103 , HOH C:1117 , HOH C:1127binding site for Di-peptide PLR C 1001 and LYS C 284
8AC8SOFTWAREGLU D:74 , ARG D:75 , SER D:98 , ALA D:143 , THR D:144 , GLY D:145 , GLN D:172 , SER D:174 , ASN D:252 , ALA D:254 , TYR D:255 , SER D:281 , LEU D:282 , ASP D:283 , ASN D:285 , GLY D:312 , ARG D:313 , ILE D:440 , HOH D:1103 , HOH D:1120binding site for Di-peptide PLR D 1001 and LYS D 284

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZDP)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:228 -Pro A:229
2Ala B:228 -Pro B:229
3Ala C:228 -Pro C:229
4Ala D:228 -Pro D:229

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZDP)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZDP)

(-) 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:444
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.........hhhhhhhhhhhhh......ee.....eee..eee.............eeeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4zdp A  20 QGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGCKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRK 463
                                    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       389       399       409       419       429       439       449       459    


Chain B from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.........hhhhhhhhhhhhh......ee.....eee..eee.............eeeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdp B  21 GCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGCKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRK 463
                                    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       380       390       400       410       420       430       440       450       460   


Chain C from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee.........hhhhhhhhhhhhh......ee.....eee..eee.............eeeee.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdp C  21 GCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGCKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRK 463
                                    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       380       390       400       410       420       430       440       450       460   


Chain D from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..............hhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh..eeeee..eee..eee.hhhhhhhhhhhhh...eeeeeee..........hhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeehhhhhh.....eeeee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeee.........hhhhhhhhhhhhh......ee.....eee..eee.............eeeee.....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zdp D  21 GCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAIMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMITAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNDSFIQEISKMYPGRASASPSLDVLITLLSLGSNGCKKLLKERKEMFSYLSNQIKKLSEAYNERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFRGFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRK 463
                                    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       380       390       400       410       420       430       440       450       460   


Chain E from PDB  Type:RNA  Length:74
                                                                                                          
                 4zdp E   1 GCCCGGAUGAUCAGUGGUCUGGGGUGCAGGACCUGUAUGUCUCGACAGAGUGGUUCAAUUCCACCUUUCGGGCG  73
                                |||  8||  ||  21        31|     |46D||||||  50        60      ||69    
                               5A||   9| 16|  |         31|    44||||||46L                  67A|      
                                5B|   13  18  |          38    46B|||||||                    67B      
                                 5C         20A                 46C||||||                             
                                                                 46D|||||                             
                                                                  46E||||                             
                                                                   46F|||                             
                                                                    46I||                             
                                                                     46J|                             
                                                                      46K
   Legend:   → Mismatch (orange background)
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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 4ZDP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZDP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZDP)

(-) Gene Ontology  (14, 14)

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 Related Entries

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

UniProtKB/Swiss-Prot
        SPCS_HUMAN | Q9HD40: 3hl2 4zdl 4zdo

(-) Related Entries Specified in the PDB File

3hl2 3HL2 CONTAINS WILD TYPE SEPSECS IN COMPLEX WITH TRNASEC
4zdl
4zdo 4ZDO CONTAINS T325S MUTANT OF SEPSECS IN COMPLEX WITH TRNASEC