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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMOSPERMIDINE SYNTHASE (HSS) FROM BLASTOCHLORIS VIRIDIS IN COMPLEX WITH NAD AND AGMATINE
 
Authors :  S. Krossa
Date :  20 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homospermidine Synthase, Oxidoreductase, Transferase, Rossman Fold, Agmatine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Krossa, A. Faust, D. Ober, A. J. Scheidig
Comprehensive Structural Characterization Of The Bacterial Homospermidine Synthase-An Essential Enzyme Of The Polyamin Metabolism.
Sci Rep V. 6 19501 2016
PubMed-ID: 26776105  |  Reference-DOI: 10.1038/SREP19501

(-) Compounds

Molecule 1 - HOMOSPERMIDINE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.44
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETM14
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: HSS
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Other Details: MET-199 IS OXIDIZED TO MHO
    Synonym: HSS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 23)

Asymmetric/Biological Unit (6, 23)
No.NameCountTypeFull Name
11PS4Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2ACT8Ligand/IonACETATE ION
3AG23Ligand/IonAGMATINE
4MHO2Mod. Amino AcidS-OXYMETHIONINE
5NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
6SO44Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:20 , SER A:21 , ILE A:22 , ASP A:45 , PRO A:46 , SER A:47 , ALA A:65 , VAL A:66 , LEU A:91 , SER A:92 , VAL A:93 , THR A:95 , THR A:114 , VAL A:115 , GLY A:160 , ALA A:161 , ASN A:162 , PRO A:163 , TRP A:229 , SER A:230 , ILE A:350 , VAL A:400 , HOH A:728 , HOH A:730 , HOH A:770 , HOH A:780 , HOH A:790 , HOH A:847 , HOH A:857 , HOH A:995binding site for residue NAD A 501
02AC2SOFTWAREVAL A:235 , ARG A:344 , HOH A:902 , HOH A:970binding site for residue ACT A 502
03AC3SOFTWARESER A:96 , PRO A:118 , TRP A:119 , HOH A:1025binding site for residue ACT A 503
04AC4SOFTWAREARG A:215 , HOH A:610 , HOH A:816 , PRO B:221binding site for residue ACT A 504
05AC5SOFTWARELYS A:343 , ARG A:344 , HOH A:946binding site for residue SO4 A 505
06AC6SOFTWAREHIS A:8 , ARG A:9 , HOH A:613 , HOH A:615 , HOH A:1031 , VAL B:76 , PRO B:77 , THR B:80binding site for residue SO4 A 506
07AC7SOFTWARECYS A:264 , ARG A:309 , ALA A:315 , ARG A:318binding site for residue SO4 A 507
08AC8SOFTWARESER A:47 , ASP A:48 , GLU A:49 , ASP A:347 , TRP A:348binding site for residue 1PS A 508
09AC9SOFTWAREVAL A:6 , GLU A:31 , ARG A:32 , PHE A:34 , PHE A:36 , HOH A:859 , HOH A:934 , HOH A:1028binding site for residue AG2 A 509
10AD1SOFTWAREGLY B:20 , SER B:21 , ILE B:22 , ASP B:45 , PRO B:46 , SER B:47 , ALA B:65 , VAL B:66 , LEU B:91 , SER B:92 , VAL B:93 , THR B:95 , THR B:114 , VAL B:115 , GLY B:160 , ALA B:161 , ASN B:162 , PRO B:163 , TRP B:229 , SER B:230 , ILE B:350 , VAL B:400 , HOH B:893 , HOH B:894 , HOH B:917 , HOH B:929 , HOH B:934 , HOH B:971 , HOH B:1012 , HOH B:1249binding site for residue NAD B 501
11AD2SOFTWAREARG B:471 , 1PS B:506 , HOH B:1086binding site for residue ACT B 502
12AD3SOFTWAREPRO A:221 , ARG B:215 , HOH B:1054 , HOH B:1130binding site for residue ACT B 503
13AD4SOFTWAREGLU A:384 , LYS B:204 , GLY B:369 , ASN B:373 , HOH B:831 , HOH B:832 , HOH B:1008binding site for residue ACT B 504
14AD5SOFTWARECYS B:264 , ARG B:309 , ALA B:315 , ARG B:318 , HOH B:1105 , HOH B:1267binding site for residue SO4 B 505
15AD6SOFTWAREGLN A:380 , VAL A:442 , VAL A:444 , ARG B:251 , ARG B:471 , ACT B:502 , HOH B:807 , HOH B:816 , HOH B:1276binding site for residue 1PS B 506
16AD7SOFTWARESER B:47 , ASP B:48 , GLU B:49 , ARG B:196 , ASP B:347 , TRP B:348binding site for residue 1PS B 507
17AD8SOFTWAREVAL B:235 , ARG B:344 , TRP B:348 , HOH B:1024 , HOH B:1102binding site for residue ACT B 508
18AD9SOFTWAREMET B:338 , GLY B:342 , LYS B:343 , ARG B:344binding site for residue 1PS B 509
19AE1SOFTWARETHR A:285 , ASP A:358 , GLY A:359 , GLU A:384 , ARG B:251 , SER B:465 , HOH B:802 , HOH B:807binding site for residue AG2 B 510
20AE2SOFTWAREGLU A:186 , HOH A:604 , GLU B:31 , ARG B:32 , PHE B:34 , PHE B:36 , ARG B:38 , HOH B:801 , HOH B:1009 , HOH B:1181binding site for residue AG2 B 511
21AE3SOFTWARESER B:167 , LYS B:171 , ILE B:302 , PHE B:305 , ASP B:423binding site for residue ACT B 512

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XR4)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:82 -Pro A:83
2Asn A:162 -Pro A:163
3Arg A:454 -Pro A:455
4Gly B:82 -Pro B:83
5Asn B:162 -Pro B:163
6Arg B:454 -Pro B:455

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XR4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XR4)

(-) Exons   (0, 0)

(no "Exon" information available for 4XR4)

(-) 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:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee....eeee..hhhhhhhhhhhhhhee.hhh.eeee..hhhhhhhhhhh..eee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhh..eee.....................hhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...eeeeeeee..ee.......eeee..hhhhhhhhhhheeeee...........ee........eeeeeee....eeeeee...eeeeee...hhhhhhhhhhh.ee.....eee..eeeeeee.hhhhhhhhhhhhhhh....eeee.hhh.eee.eeeeeeeee.....eeeeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhh..eeeeee......................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xr4 A   3 DWPVYHRIDGPIVMIGFGSIGRGTLPLIERHFAFDRSKLVVIDPSDEARKLAEARGVRFIQQAVTRDNYRELLVPLLTAGPGQGFCVNLSVDTSSLDIMELARENGALYIDTVVEPWLGFYFDPDLKPEARSNYALRETVLAARRNKPGGTTAVSCCGANPGMVSWFVKQALVNLAADLGVTGEEPTTREEWARLAmDLGVKGIHIAERDTQRASFPKPFDVFVNTWSVEGFVSEGLQPAELGWGTFERWMPDNARGHDSGCGAGIYLLQPGANTRVRSWTPTAMAQYGFLVTHNESISIADFLTVRDAAGQAVYRPTCHYAYHPCNDAVLSLHEMFGSGKRQSDWRILDETEIVDGIDELGVLLYGHGKNAYWYGSQLSIEETRRIAPDQNATGLQVSSAVLAGMVWALENPNAGIVEADDLDFRRCLEVQTPYLGPVVGVYTDWTPLAGRPGLFPEDIDTSDPWQFRNVLVR 476
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      |202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472    
                                                                                                                                                                                                                              199-MHO                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:474
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee....eeee..hhhhhhhhhhhhhhee.hhh.eeee..hhhhhhhhhhhh.eee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhh..eee................hhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeee..ee.......eeee..hhhhhhhhhhheeeee...........ee........eeeeeee....eeeeee...eeeeee...hhhhhhhhhhh.ee.....eee..eeeeeee.hhhhhhhhhhhhhhh....eeee.hhh.eee..eeeeeeee.....eeeeee..hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhh..eeeeee......................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xr4 B   3 DWPVYHRIDGPIVMIGFGSIGRGTLPLIERHFAFDRSKLVVIDPSDEARKLAEARGVRFIQQAVTRDNYRELLVPLLTAGPGQGFCVNLSVDTSSLDIMELARENGALYIDTVVEPWLGFYFDPDLKPEARSNYALRETVLAARRNKPGGTTAVSCCGANPGMVSWFVKQALVNLAADLGVTGEEPTTREEWARLAmDLGVKGIHIAERDTQRASFPKPFDVFVNTWSVEGFVSEGLQPAELGWGTFERWMPDNARGHDSGCGAGIYLLQPGANTRVRSWTPTAMAQYGFLVTHNESISIADFLTVRDAAGQAVYRPTCHYAYHPCNDAVLSLHEMFGSGKRQSDWRILDETEIVDGIDELGVLLYGHGKNAYWYGSQLSIEETRRIAPDQNATGLQVSSAVLAGMVWALENPNAGIVEADDLDFRRCLEVQTPYLGPVVGVYTDWTPLAGRPGLFPEDIDTSDPWQFRNVLVR 476
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192      |202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472    
                                                                                                                                                                                                                              199-MHO
   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 4XR4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XR4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XR4)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  HSS_BLAVI | O32323
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  2.5.1.44
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 Related Entries

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

UniProtKB/Swiss-Prot
        HSS_BLAVI | O32323: 4plp 4tvb 4xq9 4xqc 4xqe 4xqg 4xrg

(-) Related Entries Specified in the PDB File

4plp 4PLP CONTAINS THE SAME PROTEIN WITHOUT AG2
4tvb 4TVB CONTAINS THE SAME PROTEIN WITH PUT/37Z