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(-) Description

Title :  STRUCTURE OF HMUO, HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE, IN COMPLEX WITH THE PUTATIVE REACTION INTERMEDIATES BETWEEN FE3+-BILIVERDIN AND BILIVERDIN (DATA SET IV)
 
Authors :  M. Unno, M. Ikeda-Saito
Date :  21 Aug 12  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Helix, Heme Degradation, Heme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Unno, A. Ardevol, C. Rovira, M. Ikeda-Saito
Crystal Structures Of The Substrate-Free And The Product-Bound Forms Of Hmuo, A Heme Oxygenase From Corynebacterium Diphtheriae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HEME OXYGENASE
    Chains: A, B, C
    EC Number: 1.14.99.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717

 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, 14)

Asymmetric Unit (4, 14)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2BLA3Ligand/IonBILIVERDINE IX ALPHA
3FE2Ligand/IonFE (III) ION
4SO48Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ASC-1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3FE-1Ligand/IonFE (III) ION
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1ASC-1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3FE-1Ligand/IonFE (III) ION
4SO45Ligand/IonSULFATE ION
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3FE-1Ligand/IonFE (III) ION
4SO42Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:20 , BLA A:3002 , HOH A:3161BINDING SITE FOR RESIDUE FE A 3001
02AC2SOFTWARELYS A:13 , HIS A:20 , ALA A:23 , GLU A:24 , MET A:29 , LEU A:33 , TYR A:130 , VAL A:131 , GLY A:135 , SER A:138 , GLY A:139 , ARG A:177 , PHE A:201 , ASN A:204 , PHE A:208 , FE A:3001 , HOH A:3135 , HOH A:3161 , HOH A:3175BINDING SITE FOR RESIDUE BLA A 3002
03AC3SOFTWARESER A:26 , THR A:27 , HIS A:205 , HOH A:3155BINDING SITE FOR RESIDUE SO4 A 3003
04AC4SOFTWARELYS B:313 , HIS B:320 , GLU B:324 , LEU B:333 , TYR B:430 , VAL B:431 , GLY B:435 , SER B:438 , ILE B:443 , ARG B:477 , PHE B:501 , PHE B:508 , HOH B:740 , HOH B:890BINDING SITE FOR RESIDUE BLA B 601
05AC5SOFTWARESER B:326 , THR B:327 , HIS B:505 , HOH B:838 , HOH B:851BINDING SITE FOR RESIDUE SO4 B 602
06AC6SOFTWAREGLY B:367 , ALA B:369 , GLU B:370 , SER B:371 , HOH B:764 , HOH B:781 , HOH B:783BINDING SITE FOR RESIDUE SO4 B 603
07AC7SOFTWAREVAL B:382 , ARG B:385 , GLY B:459 , HOH B:722 , HOH B:869BINDING SITE FOR RESIDUE SO4 B 604
08AC8SOFTWARELYS B:470 , LYS B:473 , ARG B:477 , HOH B:862 , HOH B:879BINDING SITE FOR RESIDUE SO4 B 605
09AC9SOFTWAREVAL B:442 , ARG B:445BINDING SITE FOR RESIDUE SO4 B 606
10BC1SOFTWAREBLA C:902 , ASC C:903BINDING SITE FOR RESIDUE FE C 901
11BC2SOFTWARELYS C:613 , HIS C:620 , MET C:629 , TYR C:730 , VAL C:731 , ARG C:732 , GLY C:735 , SER C:738 , ILE C:743 , ARG C:777 , PHE C:801 , ASN C:804 , PHE C:808 , FE C:901 , ASC C:903 , HOH C:1025 , HOH C:1054 , HOH C:1062 , HOH C:1068 , HOH C:1159BINDING SITE FOR RESIDUE BLA C 902
12BC3SOFTWAREHIS C:620 , GLU C:624 , FE C:901 , BLA C:902 , HOH C:1136 , HOH C:1152BINDING SITE FOR RESIDUE ASC C 903
13BC4SOFTWAREGLY C:667 , ALA C:669 , GLU C:670 , SER C:671 , HOH C:1041 , HOH C:1051 , HOH C:1074BINDING SITE FOR RESIDUE SO4 C 904
14BC5SOFTWAREVAL C:682 , ARG C:685 , GLY C:759 , HOH C:1028BINDING SITE FOR RESIDUE SO4 C 905

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GPH)

(-) 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:209
                                                                                                                                                                                                                                                 
               SCOP domains d4gpha_ A: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gph A   5 TAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 213
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204         


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4gphb_ B: Heme oxygenase HmuO                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gph B 307 GLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 515
                                   316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506         


Chain C from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains d4gphc_ C: Heme oxygenase HmuO                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gph C 603 TATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKG 814
                                   612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812
   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  (1, 3)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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        Q54AI1_CORDP | Q54AI1: 1wzd 2z68 3i8r 3moo 4goh 4gpc 4gpf

(-) Related Entries Specified in the PDB File

1iw0 1iw1 4goh 4gpc 4gpf