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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HSCARG Y81A MUTANT
 
Authors :  Y. Li, G. Meng, X. Dai, M. Luo, X. Zheng
Date :  14 Aug 08  (Deposition) - 12 May 09  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Dai, Y. Li, G. Meng, S. Yao, Y. Zhao, Q. Yu, J. Zhang, M. Luo, X. Zheng
Nadph Is An Allosteric Regulator Of Hscarg
J. Mol. Biol. V. 387 1277 2009
PubMed-ID: 19254724  |  Reference-DOI: 10.1016/J.JMB.2009.02.049

(-) Compounds

Molecule 1 - NMRA-LIKE FAMILY DOMAIN-CONTAINING PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NMRAL1, HSCARG
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSCARG

 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  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3E5M)

(-) Sites  (0, 0)

(no "Site" information available for 3E5M)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3E5M)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:80 -Ala A:81
2Asn B:80 -Ala B:81
3Ala B:81 -Trp B:82
4Trp B:82 -Glu B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030689T23INMRL1_HUMANPolymorphism11557236A/BT23I
2UniProtVAR_030690P252LNMRL1_HUMANPolymorphism3747582A/BP252L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030689T23INMRL1_HUMANPolymorphism11557236AT23I
2UniProtVAR_030690P252LNMRL1_HUMANPolymorphism3747582AP252L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030689T23INMRL1_HUMANPolymorphism11557236BT23I
2UniProtVAR_030690P252LNMRL1_HUMANPolymorphism3747582BP252L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3E5M)

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002834291aENSE00001526041chr16:4524896-4524555342NMRL1_HUMAN-00--
1.2ENST000002834292ENSE00001293533chr16:4524167-452409474NMRL1_HUMAN1-14142A:5-14
B:4-14		10
11
1.3ENST000002834293ENSE00001010612chr16:4519466-4519228239NMRL1_HUMAN14-93802A:14-93
B:14-93		80
80
1.4ENST000002834294ENSE00001010610chr16:4516403-4516154250NMRL1_HUMAN94-177842A:94-177
B:94-177		84
84
1.5ENST000002834295ENSE00001010609chr16:4513851-4513661191NMRL1_HUMAN177-240642A:177-240
B:177-240		64
64
1.6bENST000002834296bENSE00001900515chr16:4511960-4511695266NMRL1_HUMAN241-299592A:241-298
B:241-298		58
58

(-) 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:294
 aligned with NMRL1_HUMAN | Q9HBL8 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:294
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    
          NMRL1_HUMAN     5 KLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhhh...eeeee......hhhhhhhh....ee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee..ee.hhhhh....ee......eee........eeeehhhhhhhhhhhhhhhhhhhh..eee....eehhhhhhhhhhhh....eee...hhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L---------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  -------------------------------------------------------------------------------Exon 1.4  PDB: A:94-177 UniProt: 94-177                                             ---------------------------------------------------------------Exon 1.6b  PDB: A:241-298 UniProt: 241-299 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ---------Exon 1.3  PDB: A:14-93 UniProt: 14-93                                           -----------------------------------------------------------------------------------Exon 1.5  PDB: A:177-240 UniProt: 177-240                       ---------------------------------------------------------- Transcript 1 (2)
                 3e5m A   5 KLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNAWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294    


Chain B from PDB  Type:PROTEIN  Length:295
 aligned with NMRL1_HUMAN | Q9HBL8 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:295
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293     
          NMRL1_HUMAN     4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNYWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhh..eee......hhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhh...eeeee...hhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee..ee.hhhh.....ee......eee........eeeehhhhhhhhhhhhhhhhhhhh..eee...eeehhhhhhhhhhhhhh..eee...hhhhhhh....hhhhhhhhhhhhh.....hhhhhhhhh....hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L---------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2   -------------------------------------------------------------------------------Exon 1.4  PDB: B:94-177 UniProt: 94-177                                             ---------------------------------------------------------------Exon 1.6b  PDB: B:241-298 UniProt: 241-299 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.3  PDB: B:14-93 UniProt: 14-93                                           -----------------------------------------------------------------------------------Exon 1.5  PDB: B:177-240 UniProt: 177-240                       ---------------------------------------------------------- Transcript 1 (2)
                 3e5m B   4 KKLVVVFGGTGAQGGSVARTLLEDGTFKVRVVTRNPRKKAAKELRLQGAEVVQGDQDDQVIMELALNGAYATFIVTNAWESCSQEQEVKQGKLLADLARRLGLHYVVYSGLENIKKLTAGRLAAAHFDGKGEVEEYFRDIGVPMTSVRLPCYFENLLSHFLPQKAPDGKSYLLSLPTGDVPMDGMSVSDLGPVVLSLLKMPEKYVGQNIGLSTCRHTAEEYAALLTKHTRKVVHDAKMTPEDYEKLGFPGARDLANMFRFYALRPDRDIELTLRLNPKALTLDQWLEQHKGDFNL 298
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293
   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 3E5M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E5M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E5M)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NMRL1_HUMAN | Q9HBL8)
biological process
    GO:0000050    urea cycle    The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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  Cis Peptide Bonds
    Ala B:81 - Trp B:82   [ RasMol ]  
    Asn A:80 - Ala A:81   [ RasMol ]  
    Asn B:80 - Ala B:81   [ RasMol ]  
    Trp B:82 - Glu B:83   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        NMRL1_HUMAN | Q9HBL8: 2exx 2wm3 2wmd 3dxf

(-) Related Entries Specified in the PDB File

2exx THE WIDE-TYPE PROTEIN