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(-) Description

Title :  STRUCTURE AND KINETIC ANALYSIS OF H2S PRODUCTION BY HUMAN MERCAPTOPYRUVATE SULFURTRANSFERASE
 
Authors :  M. Koutmos, K. Yamada, P. K. Yadav, T. Chiku, R. Banerjee
Date :  03 Mar 13  (Deposition) - 29 May 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Rhodanese, Transferase, 3-Mercaptopyruvate Sulfurtransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. K. Yadav, K. Yamada, T. Chiku, M. Koutmos, R. Banerjee
Structure And Kinetic Analysis Of H2S Production By Human Mercaptopyruvate Sulfurtransferase.
J. Biol. Chem. V. 288 20002 2013
PubMed-ID: 23698001  |  Reference-DOI: 10.1074/JBC.M113.466177

(-) Compounds

Molecule 1 - 3-MERCAPTOPYRUVATE SULFURTRANSFERASE
    Chains: A, B, C
    EC Number: 2.8.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: MPST, TST2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MST

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1CSS3Mod. Amino AcidS-MERCAPTOCYSTEINE
2GOL1Ligand/IonGLYCEROL
3PYR3Ligand/IonPYRUVIC ACID
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
1CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
2GOL-1Ligand/IonGLYCEROL
3PYR1Ligand/IonPYRUVIC ACID
4SO43Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
2GOL-1Ligand/IonGLYCEROL
3PYR1Ligand/IonPYRUVIC ACID
4SO41Ligand/IonSULFATE ION
Biological Unit 3 (4, 7)
No.NameCountTypeFull Name
1CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
2GOL1Ligand/IonGLYCEROL
3PYR1Ligand/IonPYRUVIC ACID
4SO44Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:36 , LEU A:38 , TYR A:108 , ARG A:188 , ARG A:197 , CSS A:248 , GLY A:249 , SER A:250 , HOH A:521 , HOH A:527BINDING SITE FOR RESIDUE PYR A 401
02AC2SOFTWARESER A:66 , ARG A:68 , PRO A:77 , GLY A:78 , HIS A:81 , HOH A:501BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARETRP A:15 , ARG A:24 , GLN A:27 , HIS A:96 , TRP C:15 , ARG C:24 , GLN C:27 , HIS C:96 , HOH C:614BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREGLN A:64 , ARG A:68BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWARETRP B:36 , TYR B:108 , ARG B:188 , ARG B:197 , CSS B:248 , GLY B:249 , SER B:250 , HOH B:538 , HOH B:551BINDING SITE FOR RESIDUE PYR B 401
06AC6SOFTWARESER B:66 , ASP B:67 , ARG B:68 , PRO B:77 , GLY B:78 , HIS B:81 , HOH B:501BINDING SITE FOR RESIDUE SO4 B 402
07AC7SOFTWARETRP C:36 , TYR C:108 , ARG C:188 , ARG C:197 , CSS C:248 , GLY C:249 , SER C:250 , HOH C:535 , HOH C:547BINDING SITE FOR RESIDUE PYR C 401
08AC8SOFTWARESER C:66 , ASP C:67 , ARG C:68 , PRO C:77 , GLY C:78 , HIS C:81 , HOH C:501BINDING SITE FOR RESIDUE SO4 C 402
09AC9SOFTWAREARG C:118 , HIS C:123 , TYR C:262 , HOH C:606BINDING SITE FOR RESIDUE SO4 C 403
10BC1SOFTWAREALA C:79 , GLU C:80 , HOH C:501 , HOH C:506 , HOH C:611BINDING SITE FOR RESIDUE SO4 C 404
11BC2SOFTWAREALA C:25 , GLY C:26 , PRO C:28 , HOH C:526BINDING SITE FOR RESIDUE SO4 C 405
12BC3SOFTWAREGLY B:207 , HIS C:204 , PRO C:206 , GLY C:207BINDING SITE FOR RESIDUE GOL C 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4JGT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JGT)

(-) 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:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4jgta1 A:9-151 automated matches                                                                                                              d4jgta2 A:152-288 automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh......eeeee....hhhhh.hhhhhhhhh.....ee..................hhhhhhhhhhhh......eeeee........hhhhhhhhhhhh....eeee.hhhhhhhhh....................hhh.eehhhhhhhhhhhh..eeee..hhhhhh..................ee.hhhhhh.......hhhhhhhhhhhh.......eeee......hhhhhhhhhhh......ee.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jgt A   9 SHVSAQWVAEALRAPRAGQPLQLLDASWYLPKLGRDARREFEERHIPGAAFFDIDQCSDRTSPYDHMLPGAEHFAEYAGRLGVGAATHVVIYDASDQGLYSAPRVWWMFRAFGHHAVSLLDGGLRHWLRQNLPLSSGKSQPAPAEFRAQLDPAFIKTYEDIKENLESRRFQVVDSRATGRFRGTEPEPRDGIEPGHIPGTVNIPFTDFLSQEGLEKSPEEIRHLFQEKKVDLSKPLVATcGSGVTACHVALGAYLCGKPDVPIYDGSWVEWYMRARPEDV 288
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
                                                                                                                                                                                                                                                                         248-CSS                                    


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4jgtb1 B:8-151 automated matches                                                                                                            d4jgtb2 B:152-288 automated matches                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhhhhhhh...eeeee....hhhhh.hhhhhhhhh.....ee..................hhhhhhhhhhhh......eeeee........hhhhhhhhhhhh....eeee.hhhhhhhhh....................hhh.eehhhhhhhhhhhh..eeee..hhhhhh..................ee.hhhhhh.......hhhhhhhhhhhh.......eeee......hhhhhhhhhhh......ee.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jgt B   8 GSHVSAQWVAEALRAPQPLQLLDASWYLPKLGRDARREFEERHIPGAAFFDIDQCSDRTSPYDHMLPGAEHFAEYAGRLGVGAATHVVIYDASDQGLYSAPRVWWMFRAFGHHAVSLLDGGLRHWLRQNLPLSSGKSQPAPAEFRAQLDPAFIKTYEDIKENLESRRFQVVDSRATGRFRGTEPEPRDGIEPGHIPGTVNIPFTDFLSQEGLEKSPEEIRHLFQEKKVDLSKPLVATcGSGVTACHVALGAYLCGKPDVPIYDGSWVEWYMRARPEDV 288
                                    17     || 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        
                                          23|                                                                                                                                                                                                                          248-CSS                                    
                                           27                                                                                                                                                                                                                                                                     


Chain C from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4jgtc1 C:9-151 automated matches                                                                                                           d4jgtc2 C:152-288 automated matches                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhhh......eeeee.......hhhhhhhhh.....ee..................hhhhhhhhhhhh......eeeee........hhhhhhhhhhhh....eeee.hhhhhhhhh....................hhh.eehhhhhhhhhhhh..eeee..hhhhhh..................ee.hhhhhh.......hhhhhhhhhhhh.......eeee.....hhhhhhhhhhhh......ee.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jgt C   9 SHVSAQWVAEALRAPRAGQPLQLLDASWYLPRDARREFEERHIPGAAFFDIDQCSDRTSPYDHMLPGAEHFAEYAGRLGVGAATHVVIYDASDQGLYSAPRVWWMFRAFGHHAVSLLDGGLRHWLRQNLPLSSGKSQPAPAEFRAQLDPAFIKTYEDIKENLESRRFQVVDSRATGRFRGTEPEPRDGIEPGHIPGTVNIPFTDFLSQEGLEKSPEEIRHLFQEKKVDLSKPLVATcGSGVTACHVALGAYLCGKPDVPIYDGSWVEWYMRARPEDV 288
                                    18        28        38||      51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241      |251       261       271       281       
                                                         39|                                                                                                                                                                                                          248-CSS                                    
                                                          43
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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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)

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  4jgt
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