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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TYROSINE PHOSPHATASE SHP-2 WITH Y279C MUTATION
 
Authors :  W. Qiu, A. Lin, A. Hutchinson, V. Romanov, M. Ruzanov, C. Thompson, K. La G. Kisselman, K. Battaile, N. Y. Chirgadze
Date :  03 Sep 12  (Deposition) - 04 Sep 13  (Release) - 04 Sep 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 :  Alpha/Beta Proteins, Sh2 Domain, Phosphatase Domain, Tyrosine Phosphatase Shp-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Qiu, A. Lin, A. Hutchinson, V. Romanov, M. Ruzanov, C. Thompson, K. Lam, G. Kisselman, K. Battaile, N. Y. Chirgadze
Crystal Structure Of The Tyrosine Phosphatase Shp-2 With Y279C Mutation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 11
    Chains: A, B
    EC Number: 3.1.3.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 22-560
    Gene: PTPN11, PTP2C, SHPTP2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN-TYROSINE PHOSPHATASE 1D, PTP-1D, PROTEIN-TYROSINE PHOSPHATASE 2C, PTP-2C, SH-PTP2, SHP-2, SHP2, SH-PTP3

 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  (4, 19)

Asymmetric Unit (4, 19)
No.NameCountTypeFull Name
1EDO15Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PGE-1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:4 , PHE A:7 , PHE A:41 , TYR A:63 , GLU A:252 , GLN A:255BINDING SITE FOR RESIDUE EDO A 601
02AC2SOFTWAREASN A:410 , THR A:411 , GLU A:412BINDING SITE FOR RESIDUE EDO A 603
03AC3SOFTWAREHIS A:287 , GLU A:313 , SER A:499BINDING SITE FOR RESIDUE EDO A 604
04AC4SOFTWAREGLY A:295 , ARG A:343 , VAL A:382BINDING SITE FOR RESIDUE EDO A 605
05AC5SOFTWAREVAL A:388 , GLU A:400BINDING SITE FOR RESIDUE GOL A 606
06AC6SOFTWARETYR A:396 , LEU A:398 , TYR A:418 , GLU A:441BINDING SITE FOR RESIDUE PEG A 607
07AC7SOFTWAREHIS A:394 , TYR A:396 , ASP A:437BINDING SITE FOR RESIDUE PEG A 608
08AC8SOFTWAREARG A:111 , THR A:219 , GLU A:250 , THR A:253 , LEU A:254 , GLN A:257 , PRO A:491 , LYS A:492 , GLN A:495 , HOH A:744BINDING SITE FOR RESIDUE PGE A 609
09AC9SOFTWAREARG B:4 , PHE B:7 , PHE B:41 , TYR B:63 , GLU B:252 , GLN B:255 , EDO B:609BINDING SITE FOR RESIDUE EDO B 601
10BC1SOFTWAREPRO B:312 , LYS B:325 , TYR B:327 , ILE B:474 , ASP B:477BINDING SITE FOR RESIDUE EDO B 602
11BC2SOFTWAREASP B:437 , HIS B:520 , THR B:524 , EDO B:604BINDING SITE FOR RESIDUE EDO B 603
12BC3SOFTWARETYR B:521 , LEU B:525 , ARG B:528 , EDO B:603BINDING SITE FOR RESIDUE EDO B 604
13BC4SOFTWAREARG B:351 , THR B:414 , TRP B:416 , ILE B:449BINDING SITE FOR RESIDUE EDO B 605
14BC5SOFTWARETRP B:6 , ALA B:75 , VAL B:78 , GLN B:79 , CYS B:259BINDING SITE FOR RESIDUE EDO B 606
15BC6SOFTWAREGLY B:409BINDING SITE FOR RESIDUE EDO B 607
16BC7SOFTWARESER B:391 , GLU B:400 , TRP B:416 , HOH B:737 , HOH B:786BINDING SITE FOR RESIDUE EDO B 608
17BC8SOFTWAREPHE B:41 , TYR B:63 , PHE B:251 , GLN B:506 , THR B:507 , GLU B:508 , EDO B:601 , HOH B:824BINDING SITE FOR RESIDUE EDO B 609
18BC9SOFTWAREGLY B:295 , ASP B:296 , VAL B:382 , HOH B:827BINDING SITE FOR RESIDUE EDO B 610

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:140 -Gln A:141
2His B:85 -Gly B:86

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GWF)

(-) 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:497
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4gwfa1 A:2-110 automated matches                                                                    d4gwfa2 A:111-218 automated matches                                                                d4gwfa3 A:219-535 automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh....eeeeee....eeeeeeee..eeeeeeee.....eee....ee.hhhhhhhhhhh..........ee...........eee..hhhhhhhhhhhh....eeeeee.......eeeeeee...eeeeeeeeee..eee........hhhhhhhhhhhh.ee.....ee...ee.....ee..hhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.............................eeee......eeee......hhhhhhhhhhhhh..eeee....ee..ee...........eeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeee...........hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gwf A   2 TSRRWFHPNITGVEAENLLLTRGVDGSFLARPSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEGQLKEVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRCKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQKS 535
                                    11        21        31  ||    43        53        63        73        83|   ||  99       109       119       129       139       149    || 168       178       188       198       208       218       228      |248       258       268       278       288       298       308    || 328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       
                                                           34|                                            83|  90|                                                        154|                                                                    235|                                                                313|                                                                                                                                                                                                                   
                                                            37                                             86   95                                                         164                                                                     246                                                                 324                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:493
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4gwfb1 B:3-110 automated matches                                                                     d4gwfb2 B:111-218 automated matches                                                              d4gwfb3 B:219-534 automated matches                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh...eeeeee.......eeeeeee..eeeeeeee.....eee....ee.hhhhhhhhhh...........ee...........eee..hhhhhhhhhhhh....eeeeee.......eeeeee...eeeeeeeee..eee........hhhhhhhhhhhh.ee.....ee...ee.....ee..hhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhh..hhhhh.............................eeee....eeee...hhhhhhhhhhhhhhhh..eeee....ee..ee...........eeee..eeeeeeeeee...eeeeeeeeee.......eeeeeeee...........hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gwf B   3 SRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAELVQYYMEHHGQLVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRCKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQK 534
                                    12        22        32        42        52        62        72        82     || 98       108       118       128       138       148     ||169       179       189       199       209       219       229     ||249       259       269       279       289       299       309  ||   331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
                                                                                                                88|                                                        154|                                                                  235|                                                               312|                                                                                                                                                                                                                 
                                                                                                                 95                                                         166                                                                   246                                                                325
   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  (2, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (78, 78)

Asymmetric Unit(hide GO term definitions)

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  4gwf
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        PTN11_HUMAN | Q06124: 2shp 3b7o 3mow 3o5x 3tkz 3tl0 3zm0 3zm1 3zm2 3zm3 4dgp 4dgx 4h1o 4h34 4je4 4jeg 4jmg 4nwf 4nwg 4ohd 4ohe 4ohh 4ohi 4ohl 4pvg 4qsy 4rdd 5df6 5ehp 5ehr 5i6v 5ibm 5ibs

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