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(-) Description

Title :  STRUCTURE OF THE BILIVERDIN-HMUO, HEME OXYGENASE FROM CORYNEBACTERIUM DIPHTHERIAE
 
Authors :  M. Unno, M. Ikeda-Saito
Date :  20 Aug 12  (Deposition) - 21 Aug 13  (Release) - 21 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2BLA3Ligand/IonBILIVERDINE IX ALPHA
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ASC-1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1ASC-1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3SO43Ligand/IonSULFATE ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
1ASC1Ligand/IonASCORBIC ACID
2BLA1Ligand/IonBILIVERDINE IX ALPHA
3SO41Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS 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 , ILE A:143 , ARG A:177 , PHE A:201 , ASN A:204 , PHE A:208 , HOH A:1052 , HOH A:1057 , HOH A:1058 , HOH A:1089 , HOH A:1103BINDING SITE FOR RESIDUE BLA A 901
02AC2SOFTWAREALA A:167 , LYS A:168 , LEU A:169 , LYS A:170BINDING SITE FOR RESIDUE SO4 A 902
03AC3SOFTWARETHR A:27 , HIS A:205 , ALA A:209BINDING SITE FOR RESIDUE SO4 A 903
04AC4SOFTWARELYS B:313 , HIS B:320 , ALA B:323 , GLU B:324 , 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:733 , HOH B:830 , HOH B:833 , HOH B:841BINDING SITE FOR RESIDUE BLA B 601
05AC5SOFTWAREVAL B:382 , ARG B:385 , GLY B:459 , HOH B:723BINDING SITE FOR RESIDUE SO4 B 602
06AC6SOFTWARELYS B:470 , LYS B:473 , ARG B:477 , HOH B:865 , HOH B:867BINDING SITE FOR RESIDUE SO4 B 603
07AC7SOFTWARESER B:326 , THR B:327 , HIS B:505 , HOH B:819BINDING SITE FOR RESIDUE SO4 B 604
08AC8SOFTWARELYS C:613 , HIS C:620 , GLU C:624 , MET C:629 , TYR C:730 , VAL C:731 , ARG C:732 , GLY C:735 , SER C:738 , GLY C:739 , ILE C:743 , ARG C:777 , PHE C:801 , ASN C:804 , PHE C:808 , ASC C:902 , HOH C:1022 , HOH C:1036 , HOH C:1079 , HOH C:1109BINDING SITE FOR RESIDUE BLA C 901
09AC9SOFTWAREHIS C:620 , GLU C:624 , BLA C:901 , HOH C:1139BINDING SITE FOR RESIDUE ASC C 902
10BC1SOFTWAREASN C:691 , GLU C:695 , TRP C:696 , ARG C:699BINDING SITE FOR RESIDUE SO4 C 903

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GPC)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains d4gpca_ A: Heme oxygenase HmuO                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpc A   4 ATAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 215
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213  


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains d4gpcb_ B: Heme oxygenase HmuO                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpc B 305 TAGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGKGL 515
                                   314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514 


Chain C from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains d4gpcc_ C: Heme oxygenase HmuO                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gpc C 606 AGLAVELKQSTAQAHEKAEHSTFMSDLLKGRLGVAEFTRLQEQAWLFYTALEQAVDAVRASGFAESLLDPALNRAEVLARDLDKLNGSSEWRSRITASPAVIDYVNRLEEIRDNVDGPALVAHHYVRYLGDLSGGQVIARMMQRHYGVDPEALGFYHFEGIAKLKVYKDEYREKLNNLELSDEQREHLLKEATDAFVFNHQVFADLGK 813
                                   615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805
   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 4GPC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

1iw0 1iw1 4goh 4gpf 4gph