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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN AP4A HYDROLASE E58A MUTANT
 
Authors :  H. Ge, X. Chen
Date :  10 Dec 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nudix Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ge, X. Chen, W. Yang, L. Niu, M. Teng
Crystal Structure Of Wild-Type And Mutant Human Ap4A Hydrolase.
Biochem. Biophys. Res. Commun. V. 432 16 2013
PubMed-ID: 23384440  |  Reference-DOI: 10.1016/J.BBRC.2013.01.095

(-) Compounds

Molecule 1 - BIS(5'-NUCLEOSYL)-TETRAPHOSPHATASE [ASYMMETRICAL]
    Chains: A, B
    EC Number: 3.6.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NUDT2, APAH1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIADENOSINE 5',5'''-P1,P4-TETRAPHOSPHATE ASYMMETRICAL HYDROLASE, AP4A HYDROLASE, AP4AASE, DIADENOSINE TETRAPHOSPHATASE, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 2, NUDIX MOTIF 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3PO4-1Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3PO41Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:22 , ALA A:23 , ILE A:24 , GLU A:46 , HIS A:139 , HOH A:314BINDING SITE FOR RESIDUE GOL A 201
2AC2SOFTWAREARG A:12 , TRP A:116 , HOH A:318 , TYR B:114 , TRP B:116 , HOH B:301 , HOH B:303 , HOH B:304 , HOH B:305BINDING SITE FOR RESIDUE PO4 B 201
3AC3SOFTWAREASP A:50 , GLU A:53 , GLN A:140 , LYS B:77 , TRP B:94BINDING SITE FOR RESIDUE MG B 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ICK)

(-) 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:147
                                                                                                                                                                                   
               SCOP domains d4icka_ A: automated matches                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..........eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeeeee..eeeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ick A   4 RACGLIIFRRCLIPKVDNNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRATQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEALEH 150
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       


Chain B from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains d4ickb_ B: automated matches                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.......eeeeeeee......ee..eee.....hhhhhhhhhhhhhhh.hhh.eeeeeeeeeeeeee....eeeeeeeeeee............eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ick B   3 LRACGLIIFRRCLIPKNAIEFLLLQASDGIHHWTPPKGHVEPGEDDLETALRATQEEAGIEAGQLTIIEGFKRELNYVARNKPKTVIYWLAEVKDYDVEIRLSHEHQAYRWLGLEEACQLAQFKEMKAALQEGHQFLCSIEAL 148
                                    12     || 25        35        45        55        65        75        85        95       105       115       125       135       145   
                                          18|                                                                                                                              
                                           22
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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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4ick
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  AP4A_HUMAN | P50583
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  3.6.1.17
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AP4A_HUMAN | P50583: 1xsa 1xsb 1xsc 3u53 4ijx

(-) Related Entries Specified in the PDB File

3u53 CRYSTAL STRUCTURE OF HUMAN AP4A HYDROLASE