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(-) Description

Title :  HYDROGENASE MATURATING ENDOPEPTIDASE HYBD FROM E. COLI
 
Authors :  E. Fritsche, A. Paschos, H. -G. Beisel, A. Boeck, R. Huber
Date :  23 Mar 99  (Deposition) - 22 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  Hydrogenase, Maturation, Metzincins, Nickel, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Fritsche, A. Paschos, H. G. Beisel, A. Bock, R. Huber
Crystal Structure Of The Hydrogenase Maturating Endopeptidase Hybd From Escherichia Coli.
J. Mol. Biol. V. 288 989 1999
PubMed-ID: 10331925  |  Reference-DOI: 10.1006/JMBI.1999.2719
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROGENASE 2 MATURATION PROTEASE
    Chains: A, B, C, D, E, F
    EC Number: 3.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1CD6Ligand/IonCADMIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 5 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
Biological Unit 6 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:16 , ASP A:62 , HIS A:93 , HOH A:188BINDING SITE FOR RESIDUE CD A 163
2AC2SOFTWAREGLU B:16 , ASP B:62 , HIS B:93 , HOH B:189BINDING SITE FOR RESIDUE CD B 163
3AC3SOFTWAREGLU C:16 , ASP C:62 , HIS C:93BINDING SITE FOR RESIDUE CD C 163
4AC4SOFTWAREGLU D:16 , ASP D:62 , HIS D:93BINDING SITE FOR RESIDUE CD D 163
5AC5SOFTWAREGLU E:16 , ASP E:62 , HIS E:93BINDING SITE FOR RESIDUE CD E 163
6AC6SOFTWAREGLU F:16 , ASP F:62 , HIS F:93 , HOH F:192BINDING SITE FOR RESIDUE CD F 163
7CDBAUTHORGLU A:16 , ASP A:62 , HIS A:93 , GLU B:16 , ASP B:62 , HIS B:93 , GLU C:16 , ASP C:62 , HIS C:93 , GLU D:16 , ASP D:62 , HIS D:93 , GLU E:16 , ASP E:62 , HIS E:93 , GLU F:16 , ASP F:62 , HIS F:93METAL ION WAS MODELED AS A CADMIUM (FROM THE CRYSTALLIZATION BUFFER) IN VIVO: PERHAPS NICKEL.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CFZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CFZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CFZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1CFZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1CFZ)

(-) 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:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfza_ A: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzA00 A:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz A   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain B from PDB  Type:PROTEIN  Length:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfzb_ B: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzB00 B:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz B   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain C from PDB  Type:PROTEIN  Length:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfzc_ C: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzC00 C:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz C   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain D from PDB  Type:PROTEIN  Length:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfzd_ D: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzD00 D:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz D   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain E from PDB  Type:PROTEIN  Length:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfze_ E: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzE00 E:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz E   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  


Chain F from PDB  Type:PROTEIN  Length:162
 aligned with HYBD_ECOLI | P37182 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
           HYBD_ECOLI     1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPREAI 162
               SCOP domains d1cfzf_ F: Hydrogenase maturating endopeptidase HybD                                                                                                               SCOP domains
               CATH domains 1cfzF00 F:1-162 HybD-like                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh......eeeeeee...hhhhhhh....eeeeeeee.........eeeeehhhhhhhh.....hhhhhhhhhhhhhhh......eeeeeeee...........hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1cfz F   1 MRILVLGVGNILLTDEAIGVRIVEALEQRYILPDYVEILDGGTAGMELLGDMANRDHLIIADAIVSKKNAPGTMMILRDEEVPALFTNKISPHQLGLADVLSALRFTGEFPKKLTLVGVIPESLEPHIGLTPTVEAMIEPALEQVLAALRESGVEAIPRSDS 162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CFZ)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (HYBD_ECOLI | P37182)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006464    cellular protein modification process    The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
    GO:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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