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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMOSPERMIDINE SYNTHASE (HSS) VARIANT H296S FROM BLASTOCHLORIS VIRIDIS IN COMPLEX WITH NAD, PUTRESCINE AND AGMATINE
 
Authors :  S. Krossa
Date :  21 Jan 15  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homospermidine Synthase, Oxidoreductase, Transferase, Rossman Fold, Agmatine, Putrescine (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
    Mutation: YES
    Organism Scientific: BLASTOCHLORIS VIRIDIS
    Organism Taxid: 1079
    Synonym: HSS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
11PS2Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2ACT2Ligand/IonACETATE ION
3AG22Ligand/IonAGMATINE
4NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
5PUT2Ligand/Ion1,4-DIAMINOBUTANE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
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 , GLU A:237 , ILE A:350 , VAL A:400 , AG2 A:502 , PUT A:503 , HOH A:757 , HOH A:764 , HOH A:793 , HOH A:799 , HOH A:848 , HOH A:1019 , HOH A:1069 , HOH A:1138 , HOH A:1162binding site for residue NAD A 501
02AC2SOFTWAREASN A:162 , GLU A:210 , TRP A:229 , GLU A:237 , VAL A:294 , THR A:295 , SER A:296 , TYR A:323 , NAD A:501 , PUT A:503 , HOH A:1091binding site for residue AG2 A 502
03AC3SOFTWAREASN A:162 , GLU A:210 , TYR A:323 , LEU A:363 , NAD A:501 , AG2 A:502 , HOH A:1091binding site for residue PUT A 503
04AC4SOFTWARESER A:47 , ASP A:48 , GLU A:49 , ASP A:347 , TRP A:348binding site for residue 1PS A 504
05AC5SOFTWAREMET A:338 , GLY A:342 , LYS A:343 , ARG A:344binding site for residue 1PS A 505
06AC6SOFTWAREPHE B:19 , GLY B:20 , SER B:21 , ILE B:22 , ASP B:45 , PRO B:46 , 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 , GLU B:237 , ILE B:350 , VAL B:400 , AG2 B:502 , PUT B:503 , HOH B:676 , HOH B:693 , HOH B:711 , HOH B:720 , HOH B:768 , HOH B:772 , HOH B:784 , HOH B:1070 , HOH B:1097 , HOH B:1106binding site for residue NAD B 501
07AC7SOFTWAREASN B:162 , GLU B:210 , TRP B:229 , GLU B:237 , THR B:295 , SER B:296 , TYR B:323 , NAD B:501 , PUT B:503 , HOH B:871binding site for residue AG2 B 502
08AC8SOFTWAREASN B:162 , GLU B:210 , TRP B:229 , TYR B:323 , NAD B:501 , AG2 B:502 , HOH B:871binding site for residue PUT B 503
09AC9SOFTWARELYS B:171 , TRP B:194 , LEU B:425 , PHE B:427binding site for residue ACT B 504
10AD1SOFTWARESER B:167 , VAL B:170 , LYS B:171 , ILE B:302 , PHE B:305 , LEU B:306 , ASP B:423binding site for residue ACT B 505

(-) SS Bonds  (0, 0)

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

(-) 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 4XRG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XRG)

(-) 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..hhhhhhhhhhhh.eee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhh..eeee...............hhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..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
                 4xrg A   3 DWPVYHRIDGPIVMIGFGSIGRGTLPLIERHFAFDRSKLVVIDPSDEARKLAEARGVRFIQQAVTRDNYRELLVPLLTAGPGQGFCVNLSVDTSSLDIMELARENGALYIDTVVEPWLGFYFDPDLKPEARSNYALRETVLAARRNKPGGTTAVSCCGANPGMVSWFVKQALVNLAADLGVTGEEPTTREEWARLAMDLGVKGIHIAERDTQRASFPKPFDVFVNTWSVEGFVSEGLQPAELGWGTFERWMPDNARGHDSGCGAGIYLLQPGANTRVRSWTPTAMAQYGFLVTSNESISIADFLTVRDAAGQAVYRPTCHYAYHPCNDAVLSLHEMFGSGKRQSDWRILDETEIVDGIDELGVLLYGHGKNAYWYGSQLSIEETRRIAPDQNATGLQVSSAVLAGMVWALENPNAGIVEADDLDFRRCLEVQTPYLGPVVGVYTDWTPLAGRPGLFPEDIDTSDPWQFRNVLVR 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    


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..hhhhhhhhhhh..eee.......hhhhhhhhhhh......eeee.....hhhhhhhhhhhh..eeee.......hhhhh...hhhhhhhhhhhhhhhhhhhhh.....eee......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..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
                 4xrg B   3 DWPVYHRIDGPIVMIGFGSIGRGTLPLIERHFAFDRSKLVVIDPSDEARKLAEARGVRFIQQAVTRDNYRELLVPLLTAGPGQGFCVNLSVDTSSLDIMELARENGALYIDTVVEPWLGFYFDPDLKPEARSNYALRETVLAARRNKPGGTTAVSCCGANPGMVSWFVKQALVNLAADLGVTGEEPTTREEWARLAMDLGVKGIHIAERDTQRASFPKPFDVFVNTWSVEGFVSEGLQPAELGWGTFERWMPDNARGHDSGCGAGIYLLQPGANTRVRSWTPTAMAQYGFLVTSNESISIADFLTVRDAAGQAVYRPTCHYAYHPCNDAVLSLHEMFGSGKRQSDWRILDETEIVDGIDELGVLLYGHGKNAYWYGSQLSIEETRRIAPDQNATGLQVSSAVLAGMVWALENPNAGIVEADDLDFRRCLEVQTPYLGPVVGVYTDWTPLAGRPGLFPEDIDTSDPWQFRNVLVR 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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 4XRG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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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 4xr4

(-) Related Entries Specified in the PDB File

4plp 4PLP CONTAINS THE WILD-TYPE
4xqe 4XQE CONTAINS SAME PROTEIN WITHOUT PUTRESCINE