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(-) Description

Title :  CRYSTAL STRUCTURE OF TRYPTOPHAN HALOGENASE (YP_750003.1) FROM SHEWANELLA FRIGIDIMARINA NCIMB 400 AT 1.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  16 May 07  (Deposition) - 29 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Yp_750003. 1, Tryptophan Halogenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Tryptophan Halogenase (Yp_750003. 1) From Shewanella Frigidimarina Ncimb 400 At 1. 50 A Resolutio
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRYPTOPHAN HALOGENASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_750003.1, SFRI_1312
    Organism Scientific: SHEWANELLA FRIGIDIMARINA
    Organism Taxid: 318167
    Strain: NCIMB 400

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 25)

Asymmetric Unit (4, 25)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MSE18Mod. Amino AcidSELENOMETHIONINE
3PG42Ligand/IonTETRAETHYLENE GLYCOL
4TLA4Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4TLA2Ligand/IonL(+)-TARTARIC ACID
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE9Mod. Amino AcidSELENOMETHIONINE
3PG41Ligand/IonTETRAETHYLENE GLYCOL
4TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:58 , ALA A:173 , HOH A:730BINDING SITE FOR RESIDUE CL A 526
2AC2SOFTWAREGLY A:15 , THR A:16 , ALA A:17 , GLY A:229 , GLY A:350 , MSE A:351 , HOH A:602 , HOH A:610 , HOH A:644 , HOH A:829 , HOH A:931 , HOH A:987 , HOH A:995 , HOH A:1301BINDING SITE FOR RESIDUE TLA A 527
3AC3SOFTWARELYS A:247 , ASP A:253 , ARG A:254 , ILE A:333 , ASN A:334 , HOH A:695 , LYS B:247 , ASP B:253 , ARG B:254 , ILE B:333 , ASN B:334 , HOH B:719 , HOH B:1263 , HOH B:1283BINDING SITE FOR RESIDUE TLA A 528
4AC4SOFTWAREGLY B:15 , THR B:16 , ALA B:17 , GLY B:229 , GLY B:350 , MSE B:351 , HOH B:611 , HOH B:659 , HOH B:739 , HOH B:746 , HOH B:955 , HOH B:1055 , HOH B:1133 , HOH B:1154 , HOH B:1332BINDING SITE FOR RESIDUE TLA B 526
5AC5SOFTWARELYS A:516 , GLN A:519 , HOH A:1023 , ARG B:81 , TYR B:520 , HOH B:832BINDING SITE FOR RESIDUE TLA B 527
6AC6SOFTWARELEU A:24 , GLU A:28 , SER A:67 , THR A:68 , LYS A:71 , GLU A:368 , SER A:372 , ALA A:375 , GLN A:376 , HOH A:553 , HOH A:999BINDING SITE FOR RESIDUE PG4 A 529
7AC7SOFTWARELEU B:24 , GLU B:28 , SER B:67 , THR B:68 , LYS B:71 , GLU B:368 , SER B:372 , GLN B:376 , HOH B:568BINDING SITE FOR RESIDUE PG4 B 528

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PYX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PYX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PYX)

(-) Exons   (0, 0)

(no "Exon" information available for 2PYX)

(-) 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:526
 aligned with Q085A0_SHEFN | Q085A0 from UniProtKB/TrEMBL  Length:525

    Alignment length:526
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        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       469       479       489       499       509       519      
         Q085A0_SHEFN     - -MMQKPITEIIIVGGGTAGWITAGLLAAEHNVDKGVLAHSPKLNITLIESPDVATIGVGEGTWPSMRSTLSKIGIDENDFIRQCDASFKQGSRFINWCKDPQSNVADSYLHPFSLPHGHQELDLCPYWLPHAEQVSFAEAVCSQQVLTQLGLAPKSIVTAQYHFQNNYGYHLNAAKFSQLLTEHCTQKLGVTHIRDHVSQIINNQHGDIEKLITKQNGEISGQLFIDCTGAKSLLLGEHLQVPFLSQKSVLFNDRALAIQVPYSDANSPIASCTHSTAQPNGWIWDIGLPTRKGVGYVYSSSHTNDIDAQKTLFNYLGVDGAAADKLEPRQLAINPGYRAKCWQNNCIAIGMAAGFIEPLEASALALIEWTASTLAQQLPPNRMVMDTISARVNERYQQHWQQIIDFLKLHYVISQRQEDRYWRDHRESNSIPDSLQAMLELWRYQTPSQQDISYKEALFPAASFQYVLYGMSFNTQLPTHVKPSMQQLAQRLFNDNQQRTQALSKNLPTNRELLDKVAQYGFPKL 525
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pyxA01 A:0-84,A:166-246,A:335-380  [code=3.50.50.60, no name defined]               ---------------------------------------------------------------------------------2pyxA01 A:0-84,A:166-246,A:335-380  [code=3.50.50.60, no name defined]           ----------------------------------------------------------------------------------------2pyxA01 A:0-84,A:166-246,A:335-380            ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eeeee.hhhhhhhhhhhhhhhhhee..ee......eeeeee..........ee..hhhhhhhhhhh.hhhhhhhhh..eee.eeeee............eeeee...........hhhhhhhhh...hhhhhhhhhhhhhhh..................eeeehhhhhhhhhhhhhhhh...eeee..eeeeee.....eeeeee....eee..eeee.hhhhh..........eeehhhhhh..eeeeeeee...........eeeeee..eeeeeee...eeeeeeee.....hhhhhhhhhhhhhh.hhhhhhhh..eeee...eee...ee..eee.hhh.ee.....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyx A   0 GmmQKPITEIIIVGGGTAGWITAGLLAAEHNVDKGVLAHSPKLNITLIESPDVATIGVGEGTWPSmRSTLSKIGIDENDFIRQCDASFKQGSRFINWCKDPQSNVADSYLHPFSLPHGHQELDLCPYWLPHAEQVSFAEAVCSQQVLTQLGLAPKSIVTAQYHFQNNYGYHLNAAKFSQLLTEHCTQKLGVTHIRDHVSQIINNQHGDIEKLITKQNGEISGQLFIDCTGAKSLLLGEHLQVPFLSQKSVLFNDRALAIQVPYSDANSPIASCTHSTAQPNGWIWDIGLPTRKGVGYVYSSSHTNDIDAQKTLFNYLGVDGAAADKLEPRQLAINPGYRAKCWQNNCIAIGmAAGFIEPLEASALALIEWTASTLAQQLPPNRmVmDTISARVNERYQQHWQQIIDFLKLHYVISQRQEDRYWRDHRESNSIPDSLQAmLELWRYQTPSQQDISYKEALFPAASFQYVLYGmSFNTQLPTHVKPSmQQLAQRLFNDNQQRTQALSKNLPTNRELLDKVAQYGFPKL 525
                             ||      9        19        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       469 |     479     | 489       499       509       519      
                             ||                                                             65-MSE                                                                                                                                                                                                                                                                                       351-MSE                         383-MSE                                                438-MSE                          471-MSE       485-MSE                                    
                             1-MSE                                                                                                                                                                                                                                                                                                                                                                                         385-MSE                                                                                                                                        
                              2-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:526
 aligned with Q085A0_SHEFN | Q085A0 from UniProtKB/TrEMBL  Length:525

    Alignment length:526
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        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       469       479       489       499       509       519      
         Q085A0_SHEFN     - -MMQKPITEIIIVGGGTAGWITAGLLAAEHNVDKGVLAHSPKLNITLIESPDVATIGVGEGTWPSMRSTLSKIGIDENDFIRQCDASFKQGSRFINWCKDPQSNVADSYLHPFSLPHGHQELDLCPYWLPHAEQVSFAEAVCSQQVLTQLGLAPKSIVTAQYHFQNNYGYHLNAAKFSQLLTEHCTQKLGVTHIRDHVSQIINNQHGDIEKLITKQNGEISGQLFIDCTGAKSLLLGEHLQVPFLSQKSVLFNDRALAIQVPYSDANSPIASCTHSTAQPNGWIWDIGLPTRKGVGYVYSSSHTNDIDAQKTLFNYLGVDGAAADKLEPRQLAINPGYRAKCWQNNCIAIGMAAGFIEPLEASALALIEWTASTLAQQLPPNRMVMDTISARVNERYQQHWQQIIDFLKLHYVISQRQEDRYWRDHRESNSIPDSLQAMLELWRYQTPSQQDISYKEALFPAASFQYVLYGMSFNTQLPTHVKPSMQQLAQRLFNDNQQRTQALSKNLPTNRELLDKVAQYGFPKL 525
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pyxB01 B:0-84,B:166-246,B:335-380  [code=3.50.50.60, no name defined]               ---------------------------------------------------------------------------------2pyxB01 B:0-84,B:166-246,B:335-380  [code=3.50.50.60, no name defined]           ----------------------------------------------------------------------------------------2pyxB01 B:0-84,B:166-246,B:335-380            ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------Trp_halogenase-2pyxB01 B:8-490                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------------------------- Pfam domains (1)
           Pfam domains (2) --------Trp_halogenase-2pyxB02 B:8-490                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ----------------------------------- Pfam domains (2)
         Sec.struct. author hhhhh...eeeee.hhhhhhhhhhhhhhhhhee..ee......eeeeee..........ee..hhhhhhhhhhh.hhhhhhhhh..eee.eeeee............eeeee...........hhhhhhhhh...hhhhhhhhhhhhhhh..................eeeehhhhhhhhhhhhhhhh...eeee..eeeeee.....eeeeee....eee..eeee.hhhhh..........eeehhhhhh..eeeeeeee...........eeeeee..eeeeeee...eeeeeeee.....hhhhhhhhhhhhhh.hhhhhhhh..eeee...eee...ee..eee.....ee.....hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyx B   0 GmmQKPITEIIIVGGGTAGWITAGLLAAEHNVDKGVLAHSPKLNITLIESPDVATIGVGEGTWPSmRSTLSKIGIDENDFIRQCDASFKQGSRFINWCKDPQSNVADSYLHPFSLPHGHQELDLCPYWLPHAEQVSFAEAVCSQQVLTQLGLAPKSIVTAQYHFQNNYGYHLNAAKFSQLLTEHCTQKLGVTHIRDHVSQIINNQHGDIEKLITKQNGEISGQLFIDCTGAKSLLLGEHLQVPFLSQKSVLFNDRALAIQVPYSDANSPIASCTHSTAQPNGWIWDIGLPTRKGVGYVYSSSHTNDIDAQKTLFNYLGVDGAAADKLEPRQLAINPGYRAKCWQNNCIAIGmAAGFIEPLEASALALIEWTASTLAQQLPPNRmVmDTISARVNERYQQHWQQIIDFLKLHYVISQRQEDRYWRDHRESNSIPDSLQAmLELWRYQTPSQQDISYKEALFPAASFQYVLYGmSFNTQLPTHVKPSmQQLAQRLFNDNQQRTQALSKNLPTNRELLDKVAQYGFPKL 525
                             ||      9        19        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       469 |     479     | 489       499       509       519      
                             1-MSE                                                          65-MSE                                                                                                                                                                                                                                                                                       351-MSE                         383-MSE                                                438-MSE                          471-MSE       485-MSE                                    
                              2-MSE                                                                                                                                                                                                                                                                                                                                                                                        385-MSE
   Legend:   → Mismatch (orange background)
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  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 2PYX)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q085A0_SHEFN | Q085A0)
molecular function
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    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.

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