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(-) Description

Title :  CYTOCHROME P450 VDH (CYP107BR1) L348M MUTANT
 
Authors :  Y. Yasutake, T. Tamura
Date :  22 Jul 16  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Oxidoreductase, Cytochrome P450 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yasutake, T. Kameda, T. Tamura
Structural Insights Into The Mechanism Of The Drastic Changes In Enzymatic Activity Of The Cytochrome P450 Vitami D3 Hydroxylase (Cyp107Br1) Caused By A Mutation Distant Fro The Active Site
Acta Crystallogr F Struct V. 73 266 2017 Biol Commun
PubMed-ID: 28471358  |  Reference-DOI: 10.1107/S2053230X17004782

(-) Compounds

Molecule 1 - VITAMIN D(3) 25-HYDROXYLASE
    Chains: A, B, C, D
    EC Number: 1.14.15.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Strain: BL21 CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: VDH
    Mutation: YES
    Organism Common: AMYCOLATA AUTOTROPHICA
    Organism Scientific: PSEUDONOCARDIA AUTOTROPHICA
    Organism Taxid: 2074
    Synonym: CYTOCHROME P450, CYP107BR1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1HEM4Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:58 , LYS A:65 , MET A:87 , HIS A:95 , ARG A:99 , LEU A:233 , ALA A:236 , GLY A:237 , THR A:240 , THR A:241 , LEU A:244 , VAL A:283 , PRO A:287 , ARG A:289 , PHE A:339 , PHE A:340 , GLY A:341 , HIS A:345 , CYS A:347 , GLY A:349 , ALA A:353 , HOH A:623binding site for residue HEM A 501
2AC2SOFTWAREPHE B:58 , LYS B:65 , MET B:87 , ILE B:88 , HIS B:95 , ARG B:99 , PHE B:106 , LEU B:233 , ALA B:236 , GLY B:237 , THR B:240 , THR B:241 , LEU B:244 , ALA B:286 , PRO B:287 , ARG B:289 , PHE B:339 , PHE B:340 , GLY B:341 , HIS B:345 , CYS B:347 , ALA B:353binding site for residue HEM B 501
3AC3SOFTWAREPHE C:58 , LYS C:65 , MET C:87 , ILE C:88 , HIS C:95 , ARG C:99 , LEU C:233 , ALA C:236 , GLY C:237 , THR C:240 , THR C:241 , PRO C:282 , PRO C:287 , ARG C:289 , PHE C:339 , PHE C:340 , GLY C:341 , ILE C:344 , HIS C:345 , CYS C:347 , GLY C:349 , ALA C:353 , HOH C:604binding site for residue HEM C 501
4AC4SOFTWAREPHE D:58 , LYS D:65 , MET D:87 , ILE D:88 , HIS D:95 , ARG D:99 , LEU D:233 , ALA D:236 , THR D:240 , THR D:241 , PRO D:282 , PRO D:287 , ARG D:289 , PHE D:339 , PHE D:340 , GLY D:341 , ILE D:344 , HIS D:345 , CYS D:347 , GLY D:349 , ALA D:353 , HOH D:626binding site for residue HEM D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GNM)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:92 -Pro A:93
2Pro B:92 -Pro B:93
3Pro C:92 -Pro C:93
4Pro D:92 -Pro D:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GNM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GNM)

(-) Exons   (0, 0)

(no "Exon" information available for 5GNM)

(-) 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:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.hhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh..ee.hhhhh.hhhhh.........hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........eee...eee..eee....eeeehhhhhh....................hhhhh.......hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gnm A   3 LTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCMGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPR 401
                                    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         


Chain B from PDB  Type:PROTEIN  Length:399
                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................hhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh..ee.hhhhhhhhhhh.........hhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh......eee......hhhhhhhhhhhhh.hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee..hhhhh..............eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gnm B   3 LTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCMGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPR 401
                                    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         


Chain C from PDB  Type:PROTEIN  Length:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhh..hhhhhhhhhhhh.eeee......eeee.hhhhhhhhh....ee.hhhhh.hhhhh.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........eee...eee..eee....eeeehhhhhh.........................hhhhh..hhhhhhhhhhhhhhhhhhhh...ee.......ee........eee.eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gnm C   3 LTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCMGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPRSA 403
                                    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 


Chain D from PDB  Type:PROTEIN  Length:401
                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh.hhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhhh..ee.hhhhhhhhhhhh...............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.....eeehhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh........eee...eee..eee....eeeehhhhhh....................hhhhh.......hhhhhhhhhhhhhhhhhhhh...ee.....................eee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gnm D   3 LTTTGTEQHDLFSGTFWQNPHPAYAALRAEDPVRKLALPDGPVWLLTRYADVREAFVDPRLSKDWRHTLPEDQRADMPATPTPMMILMDPPDHTRLRKLVGRSFTVRRMNELEPRITEIADGLLAGLPTDGPVDLMREYAFQIPVQVICELLGVPAEDRDDFSAWSSVLVDDSPADDKNAAMGKLHGYLSDLLERKRTEPDDALLSSLLAVSDEDGDRLSQEELVAMAMLLLIAGHETTVNLIGNGVLALLTHPDQRKLLAEDPSLISSAVEEFLRFDSPVSQAPIRFTAEDVTYSGVTIPAGEMVMLGLAAANRDADWMPEPDRLDITRDASGGVFFGHGIHFCMGAQLARLEGRVAIGRLFADRPELALAVGLDELVYRESTLVRGLSRMPVTMGPRSA 403
                                    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
   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 5GNM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GNM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GNM)

(-) Gene Ontology  (8, 8)

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        CPVDH_PSEAH | C4B644: 3a4g 3a4h 3a4z 3a50 3a51 3vrm 5gnl

(-) Related Entries Specified in the PDB File

5gnl